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(1S,3R,4R,5R,7S)-1-[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
?
-
-
-
-
?
(1S,3R,4R,5R,7S)-3-[4-(benzylamino)-5-methyl-2-oxopyrimidin-1(2H)-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
?
-
-
-
-
?
(1S,3R,4R,5S,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-3-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
?
-
-
-
-
?
(1S,3R,4R,5S,7S)-3-(2-acetamido-6-oxo-5,6-dihydro-9H-purin-9-yl)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
?
-
-
-
-
?
(1S,3R,4R,5S,7S)-3-[4-(benzylamino)-5-methyl-2-oxopyrimidin-1(2H)-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
?
-
-
-
-
?
(1S,3R,4R,5S,7S)-3-[6-(benzylamino)-9H-purin-9-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-ol + H2O
?
-
-
-
-
?
(1S,3R,4R,5S,7S)-3-[6-(benzylamino)-9H-purin-9-yl]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-7-yl 2-cyanoethyl N,N-dipropan-2-ylphosphoramidoite + H2O
?
-
-
-
-
?
1-[(1R,5S,7R,8S)-8-(benzyloxy)-5-[(benzyloxy)methyl]-6-oxabicyclo[3.2.1]octan-7-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
?
-
-
-
-
?
1-[(1S,3R,4R,5R,7S)-7-(benzyloxy)-1-[(benzyloxy)methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
?
-
-
-
-
?
1-[(1S,3R,4R,5R,7S)-7-[bis(4-methoxyphenyl)(phenyl)methoxy]-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
?
-
-
-
-
?
1-[(1S,3R,4R,5S,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
?
-
-
-
-
?
1-[(1S,3R,4R,5S,7S)-7-(benzyloxy)-1-[(benzyloxy)methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidine-2,4(1H,3H)-dione + H2O
?
-
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
12 basepair DNA-DNA duplex + H2O
?
12bp-RNA-DNA hybrid + H2O
?
29 basepair DNA-RNA-DNA/DNA + H2O
?
35 bp DNA-RNA-DNA/DNA chimeric hybrid + H2O
?
4-(benzylamino)-1-[(1S,3R,4R,5R,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidin-2(1H)-one + H2O
?
-
-
-
-
?
4-(benzylamino)-1-[(1S,3R,4R,5S,7S)-1-[[bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-5-methylpyrimidin-2(1H)-one + H2O
?
-
-
-
-
?
5'-(6-carboxy-fluorescein)-cggagaugacgg-3'/5'-CCGTCTCTCCG-3' + H2O
?
D13-R4-D12-D29 hybrid + H2O
?
-
-
-
?
D14R1D3:DNA18 + H2O
?
-
-
-
?
DNA*DNA + H2O
?
Tequatrovirus T4
-
5'-to 3'-exonuclease activity, degradation of DNA*DNA duplexes
-
-
?
DNA-(1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid + H2O
?
-
-
-
-
?
DNA-(2'-alkoxy-1',2'-methylene-bridged azetidine-T)-antisense-RNA hybrid + H2O
?
-
-
-
-
?
DNA-(aza-ENA-T)-antisense-RNA hybrid + H2O
?
-
-
-
-
?
DNA-(azetidine-T)-antisense-RNA hybrid + H2O
?
-
-
-
-
?
DNA-(oxetane-T)-antisense-RNA hybrid + H2O
?
-
-
-
-
?
DNA-2'-methoxyethoxy RNA hybrid
?
-
chimeric substrates containing a central DNA region with flanking northern-biased 2'-methoxyethyl nucleotides hybridized to complementary RNA, enhanced cleavage rates are observed for the eastern-biased 2'-ara-fluorothymidine and bulge inducing N-methylthymidine modifications positioned at the 5'-DNA/3'-MOE junction as well as the southern-biased 2'-methylthiothymidine and conformationally flexible tetrafluoroindole modifications positioned at the 5'-MOE/3'-DNA junction, overview
-
-
?
DNA-2'-methoxyethoxy-antisense RNA hybrid + H2O
?
-
2'-methoxyethoxy nucleotides, positioned at the 3' and 5' poles, into the antisense oligodeoxyribonucleotide of the heteroduplex to alter the helical geometry of the substrate
-
-
?
DNA-rN1-DNA/DNA + H2O
?
-
specific cleavage by RNase HII at the 5'-side of the ribonucleotide, cleavage efficiencies of the perfectly matched DNA-rN1-DNA/DNA duplexes are higher than those carrying a mismatched ribonucleotide
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
DNA-RNA hybrid + H2O
ssDNA + 5'-phosphomonoester oligonucleotides
-
in the pause of minus strang synthesis, RNAse H degrades the RNA template, with the exception of the polypurine tract sequence, immediately upstream of U3, which serves as a primer for plus-strand synthesis
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
DNA-RNA-DNA hybrid + H2O
?
DNA-RNA-DNA/DNA hybrid + H2O
?
a duplex containing a (5')RNA-DNA(3') junction with one, three, or six ribonucleotides, i.e. DNA5-RNA1-DNA6/DNA12, DNA3-RNA3-DNA6/DNA12, and RNA6-DNA6/DNA12, and a substrate with a (5')DNA-RNA(3') junction, DNA5-RNA7/DNA12
-
-
?
DNA12-RNA1-DNA27/DNA40 hybrid + H2O
?
-
enzyme cleaves RNA20/DNA20 hybrid and DNA12-RNA1-DNA27/DNA40 hybrid substrates with similar efficiency
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
dsDNA oligonucleotide with a stretch of ribonucleotides + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
-
enzyme excises misincorporated ribonucleotides in DNA
-
-
?
dsDNA oligonucleotides with a single ribose + H2O
dsDNA oligonucleotides with 1 nt gap + 5'-monophosphate ribonucleotide
-
preferred substrate, enzyme excises misincorporated ribonucleotides in DNA, enzyme places the first 5' nick, while the second 3' cut is made by Rad27p
-
-
?
M13 DNA-RNA hybrid + H2O
?
M13 DNA/RNA hybrid + H2O
?
N-(9-[(1S,3R,4R,5S,7S)-7-(benzyloxy)-1-[(benzyloxy)methyl]-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-6-oxo-6,9-dihydro-5H-purin-2-yl)acetamide + H2O
?
-
-
-
-
?
N-benzyl-9-[(1S,3R,4R,5S,7S)-1-([bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-5-methyl-7-[(trimethylsilyl)oxy]-2-oxabicyclo[2.2.1]heptan-3-yl)-9H-purin-6-amine + H2O
?
-
-
-
-
?
N-[9-[(1S,3R,4R,5S,7S)-1-([bis(4-methoxyphenyl)(phenyl)methoxy]methyl]-7-hydroxy-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-6-oxo-6,9-dihydro-5H-purin-2-yl)acetamide + H2O
?
-
-
-
-
?
N-[9-[(1S,3R,4R,5S,7S)-7-hydroxy-1-(hydroxymethyl)-5-methyl-2-oxabicyclo[2.2.1]heptan-3-yl]-6-oxo-6,9-dihydro-5H-purin-2-yl]acetamide + H2O
?
-
-
-
-
?
peptide nucleic acid - 2'-deoxy 2'-fluoroarabinonucleic acid hybrid + H2O
?
-
chimeric oligomers possessing a single central peptide nucleic acid insert are capable of forming hybrid duplexes with complementary RNA, although with diminished thermal stability in comparison to the unmodified oligomers
-
-
?
peptide nucleic acid - DNA + H2O
?
-
chimeric oligomers possessing a single central peptide nucleic acid insert are capable of forming hybrid duplexes with complementary RNA, although with diminished thermal stability in comparison to the unmodified oligomers
-
-
?
poly(rA)/poly(dT) + H2O
?
-
-
-
?
poly-rA/poly-dT + H2O
?
-
products are short oligonucleotides with very few intermediate-sized oligonucleotides
-
?
polyA*dT36 + H2O
?
-
-
-
-
?
polyA*dT36 hybrid + H2O
?
-
-
-
-
?
RNA*2'F-ANA-DNA hybrid + H2O
?
RNA*antisense-DNA hybrid + H2O
?
RNA*DNA hybrid + H2O
5'-phospho-3'-hydroxyoligonucleotides
-
specifically degrades the RNA moiety
-
-
?
RNA*DNA hybrid + H2O
DNA + 5'-phosphonucleotides
Tequatrovirus T4
-
5'-to 3'-exonuclease activity, degradation of RNA*DNA duplexes
-
-
?
RNA-DNA heteroduplex + H2O
?
the enzyme digests an RNA-RNA duplex in the presence of Mn2+
-
-
?
RNA-DNA heteroduplex + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
RNA-DNA hybrid HTS-1 + H2O
?
5'-GAUCUGAGCCUGGGAGCU-fluorescein-3' annealed to 5'-Dabcyl-AGCTCCCAGGCTCAGATC-3'
-
-
?
RNA-DNA hybrid HTS-2 + H2O
?
5'-CUGGUUAGACCAGAUCUGAGCCUGGGAGCU-fluorescein-3' annealed to 5'-Dabcyl-AGCTCCCAGGCTCAGATC-3'
-
-
?
RNA-DNA single-stranded chimera + H2O
?
-
-
-
?
RNA-DNA*DNA hybrid + H2O
8mer oligonucleotide
7 M urea-denatured 18mer, no activity with untreated hybrid, specific removal of the RNA portion of the duplex
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
RNA-DNA*DNA hybrid + H2O
oligonucleotides
7 M urea-denatured 37mer, no activity with untreated hybrid, specific removal of the RNA portion of the duplex
a 20mer, a 10mer, a 9mer, and a 7mer
-
?
RNA-DNA/DNA hybrid + H2O
?
-
PabRNase HII acts as a specific endonuclease on RNA-DNA/DNA duplexes. Specific cleavage, one nucleotide upstream of the RNA-DNA junction, occurs on a substrate in which RNA initiators is fully annealed to the cDNA template. Additionally, PabRNase HII cleaves a single ribonucleotide embedded in a double-stranded DNA
-
-
?
RNA18:DNA18 + H2O
?
-
-
-
?
RNA20/DNA20 hybrid + H2O
?
-
enzyme cleaves RNA20/DNA20 hybrid and DNA12-RNA1-DNA27/DNA40 hybrid substrates with similar efficiency
-
?
single-stranded RNA + H2O
?
-
isoenzyme C-1 and C-2 specifically act on the RNA moiety of RNA-DNA hybrid, isoenzyme C-3 degrades single-stranded RNA as well as the RNA of hybrids
-
-
?
ssDNA-dsDNA + H2O
?
Tequatrovirus T4
-
5'-to 3'-exonuclease activity, exonuclease activity removing short oligonucleotides of 3-30 nucleotides from adjacent DNA
-
-
?
[(1S,3R,4R,5S,7S)-3-[6-(benzylamino)-9H-purin-9-yl]-5-methyl-7-[(trimethylsilyl)oxy]-2-oxabicyclo[2.2.1]heptan-1-yl]methanol + H2O
?
-
-
-
-
?
additional information
?
-
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
12 basepair DNA-DNA duplex + H2O
?
oligomeric substrate, cleavage at multiple sites, product identification
-
-
?
12 basepair DNA-DNA duplex + H2O
?
-
oligomeric substrate, cleavage at multiple sites, product identification
-
-
?
12bp-RNA-DNA hybrid + H2O
?
-
RNase HII cleaves the 12 bp RNA-DNA substrate at multiple sites, but RNase HIII at only one site
-
-
?
12bp-RNA-DNA hybrid + H2O
?
-
RNase HII cleaves the 12 bp RNA-DNA substrate at multiple sites, but RNase HIII at only one site
-
-
?
29 basepair DNA-RNA-DNA/DNA + H2O
?
oligomeric substrate, cleavage mainly in the middle of the tetraribonucleotide, product identification
-
-
?
29 basepair DNA-RNA-DNA/DNA + H2O
?
-
oligomeric substrate, cleavage mainly in the middle of the tetraribonucleotide, product identification
-
-
?
35 bp DNA-RNA-DNA/DNA chimeric hybrid + H2O
?
-
-
-
-
?
35 bp DNA-RNA-DNA/DNA chimeric hybrid + H2O
?
-
-
-
-
?
5'-(6-carboxy-fluorescein)-cggagaugacgg-3'/5'-CCGTCTCTCCG-3' + H2O
?
the enzyme cleaves 12-bp RNA/DNA at multiple sites between the 3rd and 11th residues, but most preferentially at c10g11 and less preferentially at g5a6 and u7g8. The cleavage pattern of Mg2+-dependent activity is the same as that of Co2+-dependent activity, but different from that of Mn2+-dependent activity
-
-
?
5'-(6-carboxy-fluorescein)-cggagaugacgg-3'/5'-CCGTCTCTCCG-3' + H2O
?
the enzyme cleaves 12-bp RNA/DNA at multiple sites between the 3rd and 11th residues, but most preferentially at c10g11 and less preferentially at g5a6 and u7g8. The cleavage pattern of Mg2+-dependent activity is the same as that of Co2+-dependent activity, but different from that of Mn2+-dependent activity
-
-
?
DNA-RNA duplex + H2O
?
-
specific cleavage of the RNA part
-
-
?
DNA-RNA duplex + H2O
?
-
-
-
-
?
DNA-RNA duplex + H2O
?
-
the enzyme cleaves RNA exclusively in a DNA-RNA heteroduplex, cleavage pattern and site specificity dependent on the substrate structure, overview
-
-
?
DNA-RNA duplex + H2O
?
-
specific cleavage of the RNA part
-
-
?
DNA-RNA hybrid + H2O
?
-
-
-
-
?
DNA-RNA hybrid + H2O
?
-
-
-
?
DNA-RNA hybrid + H2O
?
-
RNase HII specifically catalyses the hydrolysis of phosphate diester linkages contained within the RNA portion of DNA/RNA hybrids, usage of 5'-fluorescent oligodeoxynucleotide substrates
-
-
?
DNA-RNA hybrid + H2O
?
Halalkalibacterium halodurans
-
-
-
?
DNA-RNA hybrid + H2O
?
-
-
-
-
?
DNA-RNA hybrid + H2O
?
-
-
-
?
DNA-RNA hybrid + H2O
?
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
RNase H binds RNA-DNA hybrid and double-stranded RNA duplexes with similar affinity, but only cleaves the RNA in the former in a specific manner, substrate recognition, overview
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
3H-labeled M13 DNA/RNA hybrid substrate, the N-terminal domain and C-terminal helix are involved in substrate binding, but the former contributes to substrate binding to a higher extent than the latter, overview
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
strategy for regulating RNA digestion by RNase H by using a light-activated DNA hairpin, overview
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
poly-rA/poly-dT substrate, RNase H1 contains an N-terminal domain termed dsRHbd or hybrid binding domain for binding both dsRNA and RNA/DNA hybrid, the RNA strand is recognized by a protein loop, which forms hydrogen bonds with the 2'-OH groups, substrate recognition and binding structure, residues, Y29, R32, R33, W43, R57, K59, K60, R72, and K73 are involved, overview
determination of reaction products with less than 20-nucleotides
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
-
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
-
preference for RNA-DNA hybrid but low activity towards ss and ds RNA and DNA
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
-
most active substrate: (rA)n-(dT)n
-
?
DNA-RNA-DNA hybrid + H2O
?
-
specific hydrolysis of the RNA strand of the hybrid
-
-
?
DNA-RNA-DNA hybrid + H2O
?
-
specific hydrolysis of the RNA strand of the hybrid
-
-
?
DNA/RNA hybrid + H2O
?
-
-
-
-
?
DNA/RNA hybrid + H2O
?
-
-
-
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
-
preferred substrate, enzyme excises misincorporated ribonucleotides in DNA
-
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
-
enzyme excises misincorporated ribonucleotides in DNA, enzyme places the first 5' nick, while the second 3' cut is made by FEN-1 protein
-
-
?
dsDNA oligonucleotide with a single ribose + H2O
dsDNA oligonucleotide with 1 nt gap + 5'-monophosphate ribonucleotide
-
enzyme excises misincorporated ribonucleotides in DNA
-
-
?
M13 DNA-RNA hybrid + H2O
?
-
the enzyme degrades the RNA moiety of the heteroduplex
-
-
?
M13 DNA-RNA hybrid + H2O
?
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
-
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
-
-
-
?
M13 DNA-RNA hybrid + H2O
?
-
-
-
?
M13 DNA/RNA + H2O
?
-
-
-
-
?
M13 DNA/RNA + H2O
?
-
-
-
-
?
M13 DNA/RNA hybrid + H2O
?
substrate is 3H-labeled M13 DNA/RNA hybrid
-
-
?
M13 DNA/RNA hybrid + H2O
?
-
-
-
?
poly(rAdT) + H2O
?
-
-
-
-
?
poly(rAdT) + H2O
?
-
-
-
-
?
poly(rAdT) + H2O
?
-
-
-
-
?
PPT-RNA + H2O
?
-
single-stranded, the DNA-linked enzyme mutant shows highly reduced activity compared to the wild-type enzyme, specific cleavage of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA
-
-
?
PPT-RNA + H2O
?
-
single-stranded, the DNA-linked enzyme mutant shows highly reduced activity compared to the wild-type enzyme, specific cleavage of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA
-
-
?
RNA + H2O
?
the enzyme cleaves the RNA strand of an RNA/DNA hybrid or an RNA/RNA duplex in the presence of Mn2+ or Co2+
-
-
?
RNA + H2O
?
the enzyme cleaves the RNA strand of an RNA/DNA hybrid or an RNA/RNA duplex in the presence of Mn2+ or Co2+
-
-
?
RNA*2'F-ANA-DNA hybrid + H2O
?
-
cleaves the RNA portion of hybrid duplexes of butyl-modified 2'F-ANA-DNA oligonucleotides containing acyclic interresidue units with complementary RNA
-
-
?
RNA*2'F-ANA-DNA hybrid + H2O
?
-
cleaves the RNA portion of hybrid duplexes of butyl-modified 2'F-ANA-DNA oligonucleotides containing acyclic interresidue units with complementary RNA
-
-
?
RNA*antisense-DNA hybrid + H2O
?
-
cleaves the RNA portion of hybrid duplexes of modified antisense DNA oligonucleotides containing acyclic interresidue units with complementary RNA
-
-
?
RNA*antisense-DNA hybrid + H2O
?
-
cleaves the RNA portion of hybrid duplexes of modified antisense DNA oligonucleotides containing acyclic interresidue units with complementary RNA
-
-
?
RNA*DNA hybrid + H2O
?
-
-
-
-
?
RNA*DNA hybrid + H2O
?
-
very low activity
-
-
?
RNA*DNA hybrid + H2O
?
-
specific for
-
-
?
RNA*DNA hybrid + H2O
?
-
cleaves the RNA portion
-
-
?
RNA*DNA hybrid + H2O
?
12 bp and 29 bp oligomers, cleavage site specificity depends on bound metal ion, wild-type end mutant enzymes
-
-
?
RNA*DNA hybrid + H2O
?
-
cleaves the RNA portion
-
-
?
RNA*DNA hybrid + H2O
?
-
enzyme is active only under reducing conditions, wild-type enzyme and deletion mutant H1[DELTA1-73] are inactive under oxidizing conditions
-
-
?
RNA*DNA hybrid + H2O
?
-
specific for the RNA moiety
-
-
?
RNA*DNA hybrid + H2O
?
-
the C-terminal domain of type 2 enzyme is involved in the interaction with the substrate
-
-
?
RNA*DNA hybrid + H2O
?
-
specific for
-
-
?
RNA*DNA hybrid + H2O
?
-
hydrolyses the RNA strang of the RNA*DNA heteroduplex
-
-
?
RNA-DNA duplex + H2O
?
substrate both for full-lentgh enzyme and isolated RNase H N-terminal RNase H domain
-
-
?
RNA-DNA duplex + H2O
?
substrate both for full-lentgh enzyme and isolated RNase H N-terminal RNase H domain
-
-
?
RNA-DNA duplex + H2O
?
-
-
-
?
RNA-DNA duplex + H2O
?
-
-
-
?
RNA-DNA hybrid + H2O
?
-
the enzyme could be involved in the removal of RNA primers during DNA replication
-
-
?
RNA-DNA hybrid + H2O
?
-
-
-
-
?
RNA-DNA hybrid + H2O
?
-
the enzyme may play a role in ribonucleotide excision from genomic DNA during replication
-
-
?
RNA-DNA hybrid + H2O
?
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
?
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
DNA-RNA hybrid made from phage f1 DNA
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
DNA-RNA hybrid made from phage f1 DNA
the bulk of the resulting poly(dA) obtained by cleavage of poly(dT)*poly(A4)-(dA)x still retains one covalently linked riboadenylic acid end group, a small portion carries a ribo dinucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
deoxyribotetranucleotides can still be cleaved
the bulk of the resulting poly(dA) obtained by cleavage of poly(dT)*poly(A4)-(dA)x still retains one covalently linked riboadenylic acid end group, a small portion carries a ribo dinucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
oligoribonucleotides + monoribonucleotides terminated by a 5'-phosphate
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(dT)'poly(A) in the presence of Mg2+ is the best substrate, poly(dC)'poly(G) is attacked much more slowly. Degradation velocity rises with the increasing length of the deoxyribo strand. The efficieny decreases in the following order: (dA)4-poly(U), (dG)4*poly(C), (dC)4*poly(G), (dT)4*poly(A)
the bulk of the resulting poly(dA) obtained by cleavage of poly(dT)*poly(A4)-(dA)x still retains one covalently linked riboadenylic acid end group, a small portion carries a ribo dinucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
a mixture of oligoribonucleotides with 5'-phosphate and 3'-hydroxyl terminus, oligonucleotides of various chain length, mainly 3-9 nucleotides in length
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
a mixture of oligoribonucleotides with 5'-phosphate and 3'-hydroxyl terminus, oligonucleotides of various chain length, mainly 3-9 nucleotides in length
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
hybrid between viral f1 and its complementary RNA, slight preference for cleavage adjacent to pyrimidine
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
phiX174DNA-RNA
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
digestion of more than 95% of the RNA in RNA-DNA hybrids to acid-soluble products
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
degrades only an RNA chain hydrogen bonded to DNA
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
a mixture of oligoribonucleotides with 5'-phosphate and 3'-hydroxyl terminus
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
the enzyme can hydrolyze a DNA*RNA*DNA/DNA heteroduplex that contains a single ribonucleotide
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
hybrid obtained by transcription of calf thymus DNA
oligoribonucleotides with 3'-OH and 5'-phosphate ends
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rUdA)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
oligoribonucleotides with 3'-OH and 5'-phosphate ends
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
isoenzyme C-1 and C-2 specifically act on the RNA moiety of RNA-DNA hybrid, isoenzyme C-3 degrades single-stranded RNA as well as the RNA of hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(dCrI)
oligoribonucleotides with a chain length of less than 15, having 5'-phosphate and 3'-hydroxyl end group, oligonucleotides of chain length 6-14, no mononucleotides formed
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rUdA)
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
oligoribonucleotides with a chain length of less than 15, having 5'-phosphate and 3'-hydroxyl end group, oligonucleotides of chain length 6-14, no mononucleotides formed
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
oligonucleotides with 3'-hydroxyl and 5'-phosphate termini with the structure (pA)3-9 are formed from poly(A)*poly(dT)
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
a mixture of oligonucleotides with 5'-phosphate termini and only a minor proportion of 5'-mononucleotide
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
T7 DNA-RNA hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rCdG)
mixture of oligonucleotides, ranging in size from dinucleotides to larger than hexanucleotides. No mononucleotides can be detected
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
M13 DNA:RNA[P*]DNA
oligoribonucleotides with 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rUdA)
5'-phosphorylated oligonucleotides
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rCdI)
5'-phosphorylated oligonucleotides
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
mixture of oligonucleotides, ranging in size from dinucleotides to larger than hexanucleotides. No mononucleotides can be detected
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
poly(rAdT)
5'-phosphorylated oligonucleotides
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
RNase H2 incises the DNA 5'-of the ribonucleotide, generating DNA containing 3'-hydroxyl and 5'-phosphoribonucleotide ends
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
oligonucleotides and a small amount of mononucleotides which possess 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
oligonucleotides and a small amount of mononucleotides which possess 3'-hydroxyl and 5'-phosphate termini
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
M13 DNA/RNA hybrid
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
M13 DNA/RNA hybrid
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
can degrade about 90% of the RNA strand of and RNA-DNA hybrid
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
the enzyme specifically cleaves the RNA strand of RNA/DNA hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
Halalkalibacterium halodurans
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
RNA primer recognition and removal during DNA replication
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
Tequatrovirus T4
-
enzyme removes RNA primers from lagging strand fragments during DNA replication, 5'-to 3'-exonuclease activity, degradation of the RNA portion of the duplex
-
-
?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
Tequatrovirus T4
-
specific removal of the RNA portion of the duplex
-
-
?
RNA-RNA duplex + H2O
?
substrate both for full-lentgh enzyme and isolated RNase H N-terminal RNase H domain
-
-
?
RNA-RNA duplex + H2O
?
substrate both for full-lentgh enzyme and isolated RNase H N-terminal RNase H domain
-
-
?
RNA-RNA duplex + H2O
?
reaction occurs in presence of Mn2+-ions. Residues D110, R113 and F114 are responsible for the activity, the residues are located in the region that discriminates DNA from RNA in the non-substrate strand of the duplexes
-
-
?
RNA-RNA duplex + H2O
?
weak activity. Amino acid residues Asp110, Arg113 and Phe114 of RNase HII are strongly involved in the dsRNA-digestion activity of the enzyme
-
-
?
RNA/DNA hybrid + H2O
?
model Okazaki fragment 18-mer RNA-DNA/DNA substrate (Q18), RNase H is a structure-specific endonuclease, it cleaves the 25-bp RNA/DNA hybrid at multiple sites, indicating that the enzyme cleaves RNA/DNA in a sequence-independent manner. In the absence of complementary DNA, the chimeric RNA-DNA strand is not cleaved by the enzyme
-
-
?
RNA/DNA hybrid + H2O
?
-
-
-
?
RNA/DNA hybrid + H2O
?
-
-
-
?
RNA/DNA hybrid + H2O
?
-
-
-
?
RNA/DNA hybrid + H2O
?
an RNA/DNA hybrid (RNA12/DNA12)
-
-
?
RNA/DNA hybrid + H2O
?
-
-
-
?
additional information
?
-
cleavage specificity
-
-
?
additional information
?
-
-
cleavage specificity
-
-
?
additional information
?
-
-
no attack of ribosomal RNA
-
-
?
additional information
?
-
-
no activity on natural double-stranded or single-stranded DNA, or on single-stranded RNA
-
-
?
additional information
?
-
-
stage-specific expression of RNAse H1 isozymes with different substrate specificities and divalent cation requirements, claevage specificties, overview
-
-
?
additional information
?
-
-
development of a CpRNase HII-based method for activity assay and detection: DNA-rN1-DNA fragments are modified with a fluorophore at the 5'-end and a quencher at the 3'-end to generate molecular beacons, which hybridize with single-stranded DNA to be cleaved by CpRNase HII, the method is suitable for large-scale genotyping, overview
-
-
?
additional information
?
-
-
substrate specificity and involved active site residues of RNases HII and HIII, overview
-
-
?
additional information
?
-
-
the enzyme can cleave a DNA-rN1-DNA/DNA substrate (rN1, one ribonucleotide) in vitro, e.g. a RNA-DNA hybrid consisting of CGTCCCaCCGTGC and aucagaaaaAGAGCG strands (capital letters and small bold letters represent DNA and RNA, respectively)
-
-
?
additional information
?
-
-
the enzyme can cleave a DNA-rN1-DNA/DNA substrate (rN1, one ribonucleotide) in vitro, e.g. a RNA-DNA hybrid consisting of CGTCCCaCCGTGC and aucagaaaaAGAGCG strands (capital letters and small bold letters represent DNA and RNA, respectively)
-
-
?
additional information
?
-
-
substrate specificity and involved active site residues of RNases HII and HIII, overview
-
-
?
additional information
?
-
-
no degradation of single stranded RNA
-
-
?
additional information
?
-
-
no degradation of single stranded RNA
-
-
?
additional information
?
-
recombinant EcRNH produced as a soluble form in Escherichia coli shows enzymatic activity to cleave the 3'-O-P bond of RNA in a DNA-RNA duplex, producing 3'-hydroxyl and 5'-phosphate
-
-
?
additional information
?
-
-
recombinant EcRNH produced as a soluble form in Escherichia coli shows enzymatic activity to cleave the 3'-O-P bond of RNA in a DNA-RNA duplex, producing 3'-hydroxyl and 5'-phosphate
-
-
?
additional information
?
-
-
substrate specificity
-
-
?
additional information
?
-
-
the enzyme cannot cleave the phosphodiester bond covalently linking ribonucleotides to DNA
-
-
?
additional information
?
-
-
substrate characterizationa and substrate specificity
-
-
?
additional information
?
-
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
?
additional information
?
-
-
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
?
additional information
?
-
-
determination of RNase H cleavage potential of the RNA strand basepaired with the complementary antisense oligonucleotides containing North-East conformationally constrained 1',2'-methylene-bridged azetidine-T and oxetane-T nucleosides, North-constrained 2',4'-ethylene-bridged aza-ENA-T nucleoside, and 2'-alkoxy modified nucleosides, i.e. 2'-O-Me-T and 2'-O-MOE-T modifications, molecular dynamics, overview
-
-
?
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids
-
-
?
additional information
?
-
ribonuclease H (RNase H) is an endoribonuclease that specifically cleaves the RNA strand of RNA/DNA hybrids1. It cleaves the PO-3' bond of the substrate with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function
-
-
?
additional information
?
-
-
ribonuclease H (RNase H) is an endoribonuclease that specifically cleaves the RNA strand of RNA/DNA hybrids1. It cleaves the PO-3' bond of the substrate with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function
-
-
?
additional information
?
-
cleavage of R9-D9*/D18, R2-D9*/D18, R1-D9*/D18, *D8-R1-D9/D18, D8-R1-D9*/D18, and *D18/D18 duplexes substrates by Escherichia coli RNase H1. Escherichia coli RNase H1 cleaves an Okazaki fragment-like substrate most effectively at R(-2)-R(-1) and less effectively at the RNA-DNA junction in the presence of 5 mM MnCl2, indicating that the RNase H1 exhibits a weak 3'-JRNase activity for this substrate in the presence of manganese ions
-
-
?
additional information
?
-
-
cleavage of R9-D9*/D18, R2-D9*/D18, R1-D9*/D18, *D8-R1-D9/D18, D8-R1-D9*/D18, and *D18/D18 duplexes substrates by Escherichia coli RNase H1. Escherichia coli RNase H1 cleaves an Okazaki fragment-like substrate most effectively at R(-2)-R(-1) and less effectively at the RNA-DNA junction in the presence of 5 mM MnCl2, indicating that the RNase H1 exhibits a weak 3'-JRNase activity for this substrate in the presence of manganese ions
-
-
?
additional information
?
-
-
substitution of a single native nucleotide in the antisense strand (AON) by locked nucleic acid (LNA) or by diastereomerically pure carba-LNA results in site-dependent modulation of RNase H1 promoted cleavage of complementary mRNA strands by 2 to 5 fold at 5'-GpN-3' cleavage sites, giving up to 70% of the RNA cleavage products. The 2nd best cleavage site, being the 5'-ApN-3' sites, cleaves up to 23%, depending upon the substitution site in 36 isosequential complementary AONs. A comparison of the modified AON promoted RNA cleavage rates with that of the native AON shows that sequence-specificity is considerably enhanced as a result of modification. Clearly, relatively weaker 5'-purine (Pu)-pyrimidine (Py)-3' stacking in the complementary RNA strand is preferred (giving about 90% of total cleavage products), which plays an important role in RNase H promoted RNA cleavage. A plausible mechanism of RNase H mediated cleavage of the RNA has been proposed to be 2fold, dictated by the balancing effect of the aromatic character of the purine aglycone: first, the locally formed 9-guanylate ion alters the adjoining sugar-phosphate backbone around the scissile phosphate, transforming its sugar N/S conformational equilibrium, to preferential S-type, causing preferential cleavage at 5'-GpN-3' sites around the center of 20 mer complementary mRNA. Second, the weaker nearest-neighbor strength of 5'-Pu-p-Py-3' stacking promotes preferential 5'-GpN-3' and 5'-ApN-3' cleavage, providing about 90% of the total products, compared to about 50% in that of the native one, because of the cLNA/LNA substituent effect on the neighboring 5'-Pu-p-Py-3' sites, providing both local steric flexibility and additional hydration. This facilitates both the water and water/Mg2+ ion availability at the cleavage site causing sequence-specific hydrolysis of the phosphodiester bond of scissile phosphate
-
-
?
additional information
?
-
RNase H specifically hydrolyzes the RNA strand of RNA/DNA hybrids in the presence of divalent metal ions, such as Mg2+ and Mn2+
-
-
?
additional information
?
-
-
RNase H specifically hydrolyzes the RNA strand of RNA/DNA hybrids in the presence of divalent metal ions, such as Mg2+ and Mn2+
-
-
?
additional information
?
-
model for the complex between Bst-RNase H3 and RNA/DNA hybrid and substrate binding mechanism, overview
-
-
?
additional information
?
-
-
model for the complex between Bst-RNase H3 and RNA/DNA hybrid and substrate binding mechanism, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans
member of the nucleotidyl-transferase superfamily and endo-nucleolytically cleaves the RNA portion in RNA/DNA hybrids and removes RNA primers from Okazaki fragments. Enzyme binds RNA and DNA duplexes but is unable to cleave either
-
-
?
additional information
?
-
Halalkalibacterium halodurans
conformational changes upon DNA-RNA hybrid duplex substrate binding, overview
-
-
?
additional information
?
-
Halalkalibacterium halodurans
-
RNase (H)binding induces conformational changes in RNA-DNA hybrid. RNase H distorts the DNA strand of the hybrid by rotating the phosphodiester backbone around nucleotide dA6 about 5 A x02into the nucleotide binding pocket. The superimposition of the 2 RNA-DNA hybrids shows the RNA strand has a relatively similar conformation, but the DNA strand has been distorted to significantly widen the major groove of the helix. This flexibility of the DNA strand likely plays a role in substrate recognition and discrimination
-
-
?
additional information
?
-
Halalkalibacterium halodurans C-125
-
RNase (H)binding induces conformational changes in RNA-DNA hybrid. RNase H distorts the DNA strand of the hybrid by rotating the phosphodiester backbone around nucleotide dA6 about 5 A x02into the nucleotide binding pocket. The superimposition of the 2 RNA-DNA hybrids shows the RNA strand has a relatively similar conformation, but the DNA strand has been distorted to significantly widen the major groove of the helix. This flexibility of the DNA strand likely plays a role in substrate recognition and discrimination
-
-
?
additional information
?
-
-
cleavage of RNA:DNA hybrid substrate
-
-
?
additional information
?
-
-
DNA oligonucleotide (ODN)-directed RNA cleavage assays are conducted. Substrate specificity of the HBV RNaseH, overview. HBV RNaseH activity requires an DNA:RNA heteroduplex of 14 bp or more for efficient cleavage. The full-length HBV RNaseH efficiently cleaves the RNA when the ODN ranges from 20-14 nt, but little to no cleavage is observed with the 13mer. HBV RNaseH cannot cut RNA:RNA duplexes. The HBV RNaseH enzyme also shows 3'-5' exoribonuclease activity, Ec 3.1.13.2
-
-
?
additional information
?
-
-
substrate specificity
-
-
?
additional information
?
-
-
the enzyme lacks double-stranded and single-stranded RNase and DNase activities. No hydrolysis of the DNA moiety of the RNA/DNA heteroduplex
-
-
?
additional information
?
-
-
presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
-
-
?
additional information
?
-
-
the enzyme is regulated by a unique redox switch formed by adjacent Cys147 and Cys148
-
-
?
additional information
?
-
-
formation of a disulfide bond, under oxidizing conditions, between Cys147 and Cys148 results in an inactive enzyme conformation
-
-
?
additional information
?
-
-
substrate characterization and substrate specificity
-
-
?
additional information
?
-
-
no activity with a DNA or a RNA duplex
-
-
?
additional information
?
-
-
design of a light-activated DNA hairpin to control the RNase H-mediated hydrolysis of mRNA, overview
-
-
?
additional information
?
-
-
selective substrate recognition by RNase H1
-
-
?
additional information
?
-
-
substrate specificity of RNase H1 with modifies heteroduplexes, overview
-
-
?
additional information
?
-
-
both modification by unlocked nucleic acids and 4'-C-hydroxymethyl-DNA gap insertions are compatible with RNase H activity when used sparingly. Multiple 4'-C-hydroxymethyl-DNA modifications are better tolerated by RNase H than multiple unlocked nucleic acid modifications in the gap
-
-
?
additional information
?
-
-
RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
-
-
?
additional information
?
-
-
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
?
additional information
?
-
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
?
additional information
?
-
-
the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
-
?
additional information
?
-
-
substrate is [alpha-32P]ATP-labeled poly(rA)/poly(dT)
-
-
?
additional information
?
-
-
the DNA/RNA duplex SP hybrid is a substrate for the enzyme while the RP hybrid is not. Structure-activity relationship, and NMR analysis of structural features important for enzyme activity, overview. A fully RP BH3 DNA/RNA hybrid might not be a substrate for RNase H1, NMR structure. Structural analysis of stereoregular borano phosphate modifications
-
-
?
additional information
?
-
reconstitution of the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates: the process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation and are removed by Flap endonuclease 1 (FEN1)
-
-
?
additional information
?
-
-
reconstitution of the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates: the process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation and are removed by Flap endonuclease 1 (FEN1)
-
-
?
additional information
?
-
RNase H is a non-specific endonuclease which degrades selectively the RNA strand in DNA/RNA duplexes
-
-
?
additional information
?
-
RNase H1 is an RNase H enzyme capable of cleaving RNA-DNA hybrids. It can cleave hybrids that are down to approximately 6 nucleotides in length. The enzyme can also cleave Okazaki fragment-like structures, leaving approximately two ribonucleotides next to the RNA-DNA junction
-
-
?
additional information
?
-
RNaseH1-dependent antisense oligonucleotides (ASOs) activity in human cells, mechanism and regulation, overview
-
-
?
additional information
?
-
a label-free chemiluminescent (CL) aptasensor is used for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure is a DNA-RNA chimeric strand, which contains a streptavidin aptamer sequence and a blocked RNA sequence. RNase H can specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer (SA, 5'-ATT GAC CGC TGT GTG ACG CAA CAC TCA AT-3') which can be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal is generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer, method optimization, overview
-
-
?
additional information
?
-
cleavage of RNA:DNA hybrid substrate
-
-
?
additional information
?
-
-
cleavage of RNA:DNA hybrid substrate
-
-
?
additional information
?
-
degradation of cleaved mRNA fragments by RNase H1-dependent antisense oligonucleotides (ASOs). Expression of a cytoplasm-localized mutant 7SL RNA that contains a partial U16 small nucleolar RNA (snoRNA) sequence and treatement with an RNase H1-dependent antisense oligonucleotide (ASO) simultaneously reduces both the nuclear U16 snoRNA and the cytoplasmic 7SL mutant RNA as early as 30 min after transfection in an RNase H1-dependent manner. Both the 5' and 3' cleavage products of the 7SL mutant RNA are accumulated in the cytoplasm. Some ASOs can rapidly reduce mature mRNAs without reducing pre-mRNA levels, overview
-
-
?
additional information
?
-
RNase H activated cleavage of ORN3-ORN6 by incoming ribonucleotides
-
-
?
additional information
?
-
RNase H1 can process mitochondrial R-loops. RNase H1 gradually degrades R-loops in a concentration-dependent manner, generating shorter RNA species. The shorter RNA species may be involved in hybrid G-quadruplex formation, and therefore partially resistant to RNase H1 degradation. With a template lacking L-strand promoter (LSP), RNase H1 has no apparent effects on DNA synthesis and no short DNA products are observed when RNase H1 is added together with mtSSB. Priming is dependent on R-loops, the presence of LSP. No DNA synthesis from processed LSP R-loops in the absence of RNase H1. Upon addition of RNase H1, replication products with sizes between 12 and 21 nts are observed. The highest levels of DNA synthesis are observed at 2 nM of RNase H1
-
-
?
additional information
?
-
RNase H1 cleaves RNA in RNA-DNA hybrids to generate free 3'-OH and 5'-phosphate groups. The enzyme requires substrates containing at least four ribonucleotides to be active. RNase H1 cuts only between ribonucleotides, leaving at least 2 ribonucleotides attached to the 5'-end of the DNA. Nuclease activity reactions are performed on an 80 nt DNA template annealed to a 3' end labelled 52 nt chimeric oligonucleotide that contains 26 ribonucleotides followed by 26 deoxyribonucleotides (26RNA:26DNA)
-
-
?
additional information
?
-
-
RNase H1 cleaves RNA in RNA-DNA hybrids to generate free 3'-OH and 5'-phosphate groups. The enzyme requires substrates containing at least four ribonucleotides to be active. RNase H1 cuts only between ribonucleotides, leaving at least 2 ribonucleotides attached to the 5'-end of the DNA. Nuclease activity reactions are performed on an 80 nt DNA template annealed to a 3' end labelled 52 nt chimeric oligonucleotide that contains 26 ribonucleotides followed by 26 deoxyribonucleotides (26RNA:26DNA)
-
-
?
additional information
?
-
the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
-
-
?
additional information
?
-
the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
-
-
?
additional information
?
-
-
no activity with dT36 and polyA
-
-
?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Substrate specificity, overview
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H2 is uniquely capable of incising a single embedded rNMP. Substrate specificity, overview
-
-
?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
RNase H enzymes incise the RNA strand of RNA:DNA hybrid duplexes. They are classified as type I (H1) or type II (H2 and H3). RNase H1 requires an oligoribonucleotide tract and is unable to incise a single ribonucleotide embedded in duplex DNA. Nucleis acid substrate specificity, minimal RNA requirement for RnhA, RnhA is a canonical type I RNase H enzyme, overview. Cleavage of chimeric RNA-DNA strands by RnhA. RnhA does not preferentially cleave the junctions of RNA and DNA segments, and RnhA does not completely remove a ribonucleotide tract installed 3' of DNA to yield a clean DNA3'OH end. RnhA does not incise the 32P-labeled RNA single strand
-
-
?
additional information
?
-
-
ribonuclease H(70) possesses cryptic reverse transcriptase activity
-
-
?
additional information
?
-
-
ribonuclease H(70) possesses cryptic reverse transcriptase activity
-
-
?
additional information
?
-
-
substrate specificity, enzyme plays a role in the repair of misincorporated ribonucleotides rather than or in addition to processing RNA*DNA hybrid molecules
-
-
?
additional information
?
-
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
?
additional information
?
-
substrate cleavage mode of the enzyme, cleavage site specificity
-
-
?
additional information
?
-
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
-
-
?
additional information
?
-
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
-
-
?
additional information
?
-
-
the enzyme utilizes hybrid RNA/DNA as a substrate. Cleavage activity of RNase HII with different oligomeric substrates, overview
-
-
?
additional information
?
-
Tequatrovirus T4
-
regulation
-
-
?
additional information
?
-
ribonuclease H is an enzyme that specifically cleaves RNA of RNA?DNA hybrids
-
-
?
additional information
?
-
RNase H2 hydrolyzes RNA of RNA/DNA hybrids and can nick duplex DNAs containing a single ribonucleotide. It shows a unique mechanism of recognition and substrate-assisted cleavage with preference for junction substrates. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion
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?
additional information
?
-
determination of cleavage-site specificity, overview
-
-
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
DNA-RNA hybrid + H2O
ssDNA + 5'-phosphomonoester oligonucleotides
-
in the pause of minus strang synthesis, RNAse H degrades the RNA template, with the exception of the polypurine tract sequence, immediately upstream of U3, which serves as a primer for plus-strand synthesis
-
-
?
DNA-RNA hybrid duplex + H2O
oligonucleotides terminated with 5'-phosphate and 3'-hydroxyl moiety
-
-
-
?
RNA-DNA heteroduplex + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
RNA-DNA/DNA hybrid + H2O
?
-
PabRNase HII acts as a specific endonuclease on RNA-DNA/DNA duplexes. Specific cleavage, one nucleotide upstream of the RNA-DNA junction, occurs on a substrate in which RNA initiators is fully annealed to the cDNA template. Additionally, PabRNase HII cleaves a single ribonucleotide embedded in a double-stranded DNA
-
-
?
ssDNA-dsDNA + H2O
?
Tequatrovirus T4
-
5'-to 3'-exonuclease activity, exonuclease activity removing short oligonucleotides of 3-30 nucleotides from adjacent DNA
-
-
?
additional information
?
-
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
12 base pair RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
DNA-RNA duplex + H2O
?
-
specific cleavage of the RNA part
-
-
?
DNA-RNA duplex + H2O
?
-
specific cleavage of the RNA part
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
-
-
-
?
DNA-RNA hybrid + H2O
DNA + 5'-phosphonucleotides
-
strategy for regulating RNA digestion by RNase H by using a light-activated DNA hairpin, overview
-
-
?
RNA*DNA hybrid + H2O
?
-
cleaves the RNA portion
-
-
?
RNA*DNA hybrid + H2O
?
-
cleaves the RNA portion
-
-
?
RNA-DNA hybrid + H2O
?
-
the enzyme could be involved in the removal of RNA primers during DNA replication
-
-
?
RNA-DNA hybrid + H2O
?
-
-
-
-
?
RNA-DNA hybrid + H2O
?
-
the enzyme may play a role in ribonucleotide excision from genomic DNA during replication
-
-
?
RNA-DNA hybrid + H2O
?
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
?
RNases H3 recognizes the 2'-OH groups of the RNA strand and detects the DNA strand by binding a phosphate group and inducing B-form conformation
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester
-
RNase H2 incises the DNA 5'-of the ribonucleotide, generating DNA containing 3'-hydroxyl and 5'-phosphoribonucleotide ends
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
the enzyme specifically cleaves the RNA strand of RNA/DNA hybrids
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
Halalkalibacterium halodurans
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
-
?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
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?
RNA-DNA hybrid + H2O
ribonucleotide 5'-phosphomonoester + ?
-
-
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?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
RNA primer recognition and removal during DNA replication
-
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?
RNA-DNA*DNA hybrid + H2O
DNA*DNA + 5'-phosphomononucleotides
Tequatrovirus T4
-
enzyme removes RNA primers from lagging strand fragments during DNA replication, 5'-to 3'-exonuclease activity, degradation of the RNA portion of the duplex
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?
additional information
?
-
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RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids
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?
additional information
?
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ribonuclease H (RNase H) is an endoribonuclease that specifically cleaves the RNA strand of RNA/DNA hybrids1. It cleaves the PO-3' bond of the substrate with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function
-
-
?
additional information
?
-
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ribonuclease H (RNase H) is an endoribonuclease that specifically cleaves the RNA strand of RNA/DNA hybrids1. It cleaves the PO-3' bond of the substrate with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function
-
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?
additional information
?
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RNase H specifically hydrolyzes the RNA strand of RNA/DNA hybrids in the presence of divalent metal ions, such as Mg2+ and Mn2+
-
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?
additional information
?
-
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RNase H specifically hydrolyzes the RNA strand of RNA/DNA hybrids in the presence of divalent metal ions, such as Mg2+ and Mn2+
-
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?
additional information
?
-
Halalkalibacterium halodurans
member of the nucleotidyl-transferase superfamily and endo-nucleolytically cleaves the RNA portion in RNA/DNA hybrids and removes RNA primers from Okazaki fragments. Enzyme binds RNA and DNA duplexes but is unable to cleave either
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?
additional information
?
-
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presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
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?
additional information
?
-
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the enzyme is regulated by a unique redox switch formed by adjacent Cys147 and Cys148
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?
additional information
?
-
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RNase H functions as an endonuclease that specifically cleaves the RNA moiety of RNA/DNA hybrids. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
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?
additional information
?
-
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the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
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?
additional information
?
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the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
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?
additional information
?
-
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the eukaryotic RNase H2 heterotrimeric complex recognizes RNA/DNA hybrids and 5'RNA-DNA3'/DNA junction hybrids as substrates with similar efficiency
-
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?
additional information
?
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reconstitution of the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates: the process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation and are removed by Flap endonuclease 1 (FEN1)
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?
additional information
?
-
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reconstitution of the replication cycle of L-strand synthesis in vitro using recombinant mitochondrial proteins and model OriL substrates: the process begins with initiation of DNA replication at OriL and ends with primer removal and ligation. RNase H1 partially removes the primer, leaving behind the last one to three ribonucleotides. These 5'-end ribonucleotides disturb ligation and are removed by Flap endonuclease 1 (FEN1)
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?
additional information
?
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RNase H is a non-specific endonuclease which degrades selectively the RNA strand in DNA/RNA duplexes
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?
additional information
?
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RNase H1 is an RNase H enzyme capable of cleaving RNA-DNA hybrids. It can cleave hybrids that are down to approximately 6 nucleotides in length. The enzyme can also cleave Okazaki fragment-like structures, leaving approximately two ribonucleotides next to the RNA-DNA junction
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?
additional information
?
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RNaseH1-dependent antisense oligonucleotides (ASOs) activity in human cells, mechanism and regulation, overview
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?
additional information
?
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the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
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?
additional information
?
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the enzyme is required for kinetoplast DNA replication in the mitochondrion, the RNase HIIC is essential for growth of promastigotes and amastigotes
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?
additional information
?
-
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
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?
additional information
?
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
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?
additional information
?
-
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
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?
additional information
?
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
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?
additional information
?
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
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?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
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?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
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?
additional information
?
-
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RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
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?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes
-
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?
additional information
?
-
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
-
-
?
additional information
?
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. Whereas RnhA does not incise an embedded mono-ribonucleotide, it can efficiently cleave within tracts of four or more ribonucleotides in duplex DNA
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?
additional information
?
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RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
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additional information
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RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
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additional information
?
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ribonuclease H is an enzyme that specifically cleaves RNA of RNA?DNA hybrids
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?
additional information
?
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RNase H2 hydrolyzes RNA of RNA/DNA hybrids and can nick duplex DNAs containing a single ribonucleotide. It shows a unique mechanism of recognition and substrate-assisted cleavage with preference for junction substrates. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion
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Co3+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Cu2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Na+
the enzyme exhibits the highest activity in the presence of 100 mm NaCl
NH4Cl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. NH4Cl is more efficient than NaCl
Ca2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Ca2+
Halalkalibacterium halodurans
binding structure
Co2+
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Co2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimum concentration of Co2+ or Ni2+ needed for aRNase HII activity is 1 mM. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Co2+
-
divalent metal required, optimal concentration: 20 mM, 70% of the activity with Mg2+
Co2+
-
with Co2+ as activator the decreasing order of preference is G, A, U, C
Co2+
-
activates cleavage of only poly(A) hybrids
Co2+
-
cobalt hexaamine activates
Co2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Co2+
-
10 mM Co2+ supports activity, with only minor inhibition observed at higher concentrations
Co2+
activates, best at 0.5 mM
Co2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions. The enzyme cleaves an RNA/RNA duplex in the presence of Mn2+ or Co2+
K+
the enzyme exhibits the highest activity in the presence of 100 mm KCl
K+
-
optimum KCl concentration of 100-150 mM
KCl
-
-
KCl
-
activates at 50 mM, inhibits at 200 mM
KCl
equally activating as NaCl
KCl
highly activating, best at 100-200 mM salt, KCl is preferred
KCl
-
activity increases with concentrations up to 50 mM
KCl
-
stimulates enzyme HB2
KCl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. KCl is more efficient than NaCl
KCl
activates best at 110 mM, preferred to NaCl
KCl
activates, best at 50 mM for the full-length enzyme, and at 10 mM for the C-terminal domain
KCl
requires 50 mm KCl for maximal activity
Mg2+
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Mg2+
highest activity in the presence of 10 mM MgCl2
Mg2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimal enzyme activities in the presence of Mg2+ or Mn2+ are 3fold to 7fold higher than that with the other two metals. Maximum aRNase HII activity is observed at concentrations of 6.4 mM Mg2+. The specific activity determined in the presence of 50 mM Mn2+ is 35% of that determined in the presence of 6.4 mM Mg2+. When Mn2+ is added in the presence of 1.6 mM Mg2+, the enzyme activity increases gradually as the Mn2+ concentration reaches 50 mM and decreases after that point. At equal concentrations of Mn2+ and Mg2+ (1.6 mM), the enzyme activity is reduced 10-fold compared to the activity in the presence of only Mg2+. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Mg2+
-
divalent cation required
Mg2+
-
Mn2+ is preferred over Mg2+
Mg2+
-
ribonuclease H IIa activity is preferentially activated by Mn2+ as opposed to Mg2+
Mg2+
-
optimal concentration: 2 mM
Mg2+
-
optimal activity at 10 mM
Mg2+
-
with Mg2+ as activator the decreasing order of preference is A, U/C, G
Mg2+
-
activates cleavage of only the hybrid combinations containing purine ribo strands
Mg2+
-
a divalent metal ion is required, dependent on the isozyme
Mg2+
-
Mg2+-dependent enzyme requires 10-15 mM Mg2+ for optimal activity
Mg2+
-
required, optimal activity at 2-4 mM
Mg2+
-
characterization of the strong magnesium-binding site
Mg2+
-
absolutely dependent on for activity, can be substituted by Mn2+
Mg2+
-
binding involves Asp10 and is pH-dependent, binds in the active site pocket of the natively folded enzyme only, stabilizes the enzyme conformation, effect of metal binding on enzyme folding kinetics
Mg2+
maximal activity at 5 mM, binds to metal ion binding site 1 not 2, required, can substitute for Mn2+
Mg2+
Mn2+ or Mg2+ are required for catalytic activity
Mg2+
-
Mg2+-dependent enzyme requires 15-20 mM Mg2+ for maximal activity
Mg2+
-
optimal activity with 10-15 mM
Mg2+
required, best at 50 mM
Mg2+
required, highest activity at 50 mM
Mg2+
the enzyme requires Mn2+ or Mg2+ ions, Mg2+ is preferred, coordinated with Asp97, Glu98, and Asp202
Mg2+
-
the optimum concentration is 10 mM
Mg2+
Halalkalibacterium halodurans
-
required
Mg2+
Halalkalibacterium halodurans
binding structure
Mg2+
Halalkalibacterium halodurans
the inability of the enzyme to cleave DNA is due to the deviating curvature of the DNA strand relative to the substrate RNA strand and the absence of Mg2+ at the active site
Mg2+
Halalkalibacterium halodurans
the two Mg2+ support the formation of a meta-stable phosphorane intermediate along the reaction
Mg2+
Halalkalibacterium halodurans
required, two Mg2+ ions are located at specific positions in the catalytic site
Mg2+
-
required, four RNaseH active site conserved carboxylates (the DEDD motif) coordinate two divalent cations, usually Mg2+
Mg2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Mg2+
-
broad optimum around 20 mM
Mg2+
required for catalysis
Mg2+
-
required, best at 10 mM
Mg2+
highest activity in presence of 5-10 mM
Mg2+
-
two Mg2+ ions in the RNase H active site, required. A two-metal ion mechanism requires that metal ion A activates a water molecule as a nucleophile and moves towards ion B, bringing the nucleophile in close proximity to the scissile bond, while metal ion B destabilizes the substrate-enzyme interaction and lowers the energy barrier to product formation
Mg2+
-
Mg2+ best supports the enzyme, with an optimal concentration of 10 mM
Mg2+
-
the enzyme is stabilized in the presence of Mg2+
Mg2+
-
optimal concentrations for the 4 enzyme forms at pH 7.6 and at pH 8.3
Mg2+
-
1:1 binding stoichiometry in absence of substrate at pH 8.0, activates, no binding to the enzyme but still weak activation without substrate at pH 6.5
Mg2+
-
enzyme form H2: requirement for divalent metal ion can be satisfied only by Mg2+. Enzyme form H1: requirement for a divalent metal ion can be satisfied by Mg2+ or with a stronger preference with Mn2+
Mg2+
-
enzyme is stimulated equally well by Mg2+, optimum concentration 5-10 mM, or Mn2+, optimum concentration 0.5-0.6 mM
Mg2+
-
the type 2 RNase H is an Mg2+ and alkaline pH-dependent enzyme
Mg2+
activates reaction with RNA-DNA heteroduplex and RNA-RNA duplex
Mg2+
-
optimal concentration is 6 mM
Mg2+
-
divalent cation required
Mg2+
-
Mg2+ is preferred over Mn2+
Mg2+
-
required, optimal concentration: 10-15 mM Mg2+
Mg2+
-
isoenzyme I and II both require 10-15 mM Mg2+ for maximal activity. Isoenzyme II is maximally activated by Mg2+, some activity with Mn2+
Mg2+
-
required, optimal concentration: 17 mM
Mg2+
-
Mg2+ activates more than Mn2+, RNase H(70)
Mg2+
-
Mn2+ activates more than Mg2+, RNase H(42)
Mg2+
-
absolute requirement for Mg2+, optimal activity at 2-6 mM MgCl2
Mg2+
-
absolute requirement for divalent cations, preferably Mg2+, optimal activity at 25 mM
Mg2+
activates, best at 5 mM
Mg2+
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
Mg2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions
Mg2+
-
Mn2+ or Mg2+ required
Mg2+
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview
Mg2+
the optimum concentration is 1 mM
Mg2+
the enzyme (Tma-RNase HI) and the C-terminal RNase H domain (Tma-CD) exhibit the highest activities in the presence of 1 mM MgCl2 and 0.1-5 mM MnCl2. Both proteins exhibit little activity (less than 0.01% of the maximal activity) in the presence of NiCl2, ZnCl2, CoCl2 or CaCl2. Tma-RNase HI prefers Mg2+ to Mn2+ because its maximal Mg2+-dependent activity is higher than its maximal Mn2+-dependent activity by 16fold. The enzyme specifically loses most of the Mg2+-dependent activity on removal of the hybrid binding domain and 87% of it by the mutation at the hybrid binding domain
Mg2+
-
dependent on, can substitute for Mg2+, activates the full length enzyme dependent on the N-terminal 47 amino acids
Mg2+
the enzyme prefers Mg2+ to Mn2+ ions for activity with maximal activity at 10 mM MgCl2
Mn2+
the enzyme exhibits the highest activity in the presence of 5 mM Mn2+, 1 mM Co2+, or 10 mM Mg2+, respectively. The specific activity of the enzyme determined with 5 mM MnCl2 is slightly higher than that determined with 10 mM MgCl2, and about 2 folds higher than that determined with 1 mM CoCl2
Mn2+
highest activity in the presence of 5 mM MnCl2
Mn2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimal enzyme activities in the presence of Mg2+ or Mn2+ are 3fold to 7fold higher than that with the other two metals. Maximum aRNase HII activity is observed at concentrations of 50 mM Mn2+. The specific activity determined in the presence of 50 mM Mn2+ is 35% of that determined in the presence of 6.4 mM Mg2+. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Mn2+
-
divalent cation required
Mn2+
-
Mn2+ is preferred over Mg2+
Mn2+
-
with Mg2+ as activator the decreasing order of preference is A, U, C, G
Mn2+
-
activates enzymatic cleavage of all hybrid combinations
Mn2+
-
optimal concentration: 25 mM, 40% of the activation with Mg2+
Mn2+
-
optimal activity at 1 mM
Mn2+
-
ribonuclease H IIa activity is preferentially activated by Mn2+ as opposed to Mg2+
Mn2+
-
a divalent metal ion is required, dependent on the isozyme
Mn2+
-
0.4 mM Mn2+ required for optimal activity, some activity with Mg2+
Mn2+
-
absolutely dependent on for activity, can be substituted by Mg2+
Mn2+
required, maximal activity at 0.002-0.005 mM, can substitute for Mg2+, activates up to 0.1 mM, inhibitory above, enzyme contains 2 metal ion binding sites 1 and 2 with regulatory influence on each other, activating metal ion binding site is site 1, inhibitory binding site is site 2, overview, mutants E48A, E48Q, D134A, and D134N have only 1 active Mn2+-binding site
Mn2+
-
activates, two single binding sites: site 1 is formed by Glu48, Asp10, and Asp70, site 2 is formed by Asp10 and Asp134, Glu48 and Asp134 are absolutely required for enzyme activation, binding structure and one-to-two metal mechanism, overview
Mn2+
Mn2+ or Mg2+ are required for catalytic activity
Mn2+
-
0.4 mM Mn2+ required for optimal activity, some activity with Mg2+
Mn2+
less active than Mg2+, best at 10 mM
Mn2+
the enzyme requires Mn2+ or Mg2+ ions, Mg2+ is preferred, coordinated with Asp97, Glu98, and Asp202
Mn2+
-
the optimum concentration is 10 mM
Mn2+
Halalkalibacterium halodurans
required
Mn2+
Halalkalibacterium halodurans
binding structure
Mn2+
-
slightly active with Mn2+
Mn2+
-
divalent metal ion required. Maximal activity is obtained with 10 mM Mg2+, 5 mM Co2+ or 0.5 mM Mn2+
Mn2+
0.1-1 mM, 20-30% of maximum activity
Mn2+
-
required, best at 1 mM
Mn2+
-
5 mM Mn2+ supports activity, with only minor inhibition observed at higher concentrations
Mn2+
-
optimal concentrations for the 4 enzyme forms at pH 7.6 and at pH 8.3
Mn2+
-
1:1 binding stoichiometry in absence of substrate at pH 8.0, best activator, maximal activity at 10 mM and pH 8.0
Mn2+
-
enzyme form H1: requirement for a divalent metal ion can be satisfied by Mg2+ or with a stronger preference with Mn2+
Mn2+
-
enzyme is stimulated equally well by Mg2+, optimum concentration 5-10 mM, or Mn2+, optimum concentration 0.5-0.6 mM
Mn2+
wild-type digests RNA-RNA duplexes in presence of Mn2+
Mn2+
the enzyme digests an RNA-RNA duplex in the presence of Mn2+, no activity in presence of Mg2+
Mn2+
-
divalent cation required
Mn2+
-
optimal concentration is 2 mM
Mn2+
-
isoenzyme II is maximally active at 0.4 mM, some activity with Mg2+
Mn2+
-
optimal concentration 0.6 mM
Mn2+
-
Mg2+ is preferred over Mn2+
Mn2+
-
divalent cation required
Mn2+
-
Mn2+ is preferred over Mg2+
Mn2+
-
Mg2+ activates more than Mn2+, RNase H(70)
Mn2+
-
Mn2+ activates more than Mg2+, RNase H(42)
Mn2+
-
cation requirement can be fullfilled to some extent by 2 mM Mn2+
Mn2+
activates, best at 1 mM, strongly preferred divalent cation
Mn2+
-
RNases hydrolyze RNA/DNA in the presence of various divalent cofactors such as Mg2+ and Mn2+
Mn2+
-
the activity of wild-type protein is stimulated by Mn2+, whereas this cation significantly inhibits the activity of C-terminal truncated mutant proteins
Mn2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions. The enzyme cleaves an RNA/RNA duplex in the presence of Mn2+ or Co2+
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
activates, less active than Mg2+
Mn2+
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview
Mn2+
the optimum concentration is 1 mM
Mn2+
the enzyme (Tma-RNase HI) and the C-terminal RNase H domain (Tma-CD) exhibit the highest activities in the presence of 1 mM MgCl2 and 0.1-5 mM MnCl2. Both proteins exhibit little activity (less than 0.01% of the maximal activity) in the presence of NiCl2, ZnCl2, CoCl2 or CaCl2. Tma-RNase HI prefers Mg2+ to Mn2+ because its maximal Mg2+-dependent activity is higher than its maximal Mn2+-dependent activity by 16fold
Mn2+
-
can substitute for Mg2+, activates N-terminally truncated mutant RNHIDELTA47 and inhibits the full length enzyme dependent on the presence of the N-terminal 47 amino acids
Mn2+
the enzyme prefers Mg2+ to Mn2+ ions for activity with maximal activity at 0.1 mM MnCl2
Mn2+
-
Mn2+ or Mg2+ required
Mn2+
-
optimal concentration: 1.2 mM
Mn2+
optimal RNase H activity in the presence of Mn2+ and not Mg2+
NaCl
-
activates at 50 mM, inhibits at 200 mM
NaCl
equally activating as KCl
NaCl
activating, best at 100-200 mM salt
NaCl
-
enzyme form H2 is mostly inactive at low salt and requires 100-200 mM concentration for maximal activity. KCl or NH4Cl is more efficient than NaCl
NaCl
activates best at 60 mM
Ni2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Optimum concentration of Co2+ or Ni2+ needed for aRNase HII activity is 1 mM. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Ni2+
-
exhibits only modest activity as cofactor
Ni2+
the enzyme cleaves an RNA strand of the 12-bp RNA/DNA hybrid at multiple sites only in the presence of Mn2+, Mg2+, Co2+ or Ni2+, but not in the presence of Cu2+, Ca2+ or Zn2+, or in the absence of divalent metal ions
Zn2+
strictly metal-dependent nuclease. It exhibits activity in the presence of Mg2+, Mn2+, Co2+ or Ni2+, whereas no activity is observed in the absence of these metal ions. Little activity is detected in the presence of other metals including Co3+, Cu2+, Zn2+, and Ca2+
Zn2+
-
exhibits only modest activity as cofactor
additional information
the enzyme exhibits little activity (less than 0.002% of the maximal activity) in the presence of ZnCl2, CaCl2, CoCl2 and NiCl2
additional information
metal coordination in the active site
additional information
-
metal coordination in the active site
additional information
-
the enzyme exists in two different conformations depending on the type of divalent cation activation
additional information
metal ion binding sites are located in the active site
additional information
-
metal ion binding sites are located in the active site
additional information
-
no activity in absence of Mg2+ or Mn2+, and in presence of 10 mM of Ba2+, Ca2+, Co2+, Zn2+, Cu2+, Fe2+, or Sr2+
additional information
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
-
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
Mg2+ cannot be substituted by Co2+ and Ni2+, and only partially by Mn2+
additional information
-
Mg2+ cannot be substituted by Co2+ and Ni2+, and only partially by Mn2+
additional information
Halalkalibacterium halodurans
the enzyme performs a two-metal catalysis, with metal A activating the nucleophile and metal B stabilizing the transition state, mechanism and structures, overview
additional information
Halalkalibacterium halodurans
the enzyme uses two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids
additional information
the enzyme requires either salt or divalent metal ions for folding. The enzyme exhibits activity in the presence of divalent metal ions regardless of the presence or absence of 3 M NaCl. However, higher concentrations of divalent metal ions are required for activity in the absence of salt to facilitate folding
additional information
-
enzyme requires divalent cations
additional information
-
not stimulated by Ca2+
additional information
-
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
-
enzyme is divalent metal ion-dependent, one metal ion binding mechanism, pH-dependence, kinetics, and thermodynamics for Mg2+, Mn2+, wild-type and mutant enzymes, substrate is involved in metal ion positioning and binding, Ca2+ and Ba2+ cannot substitute for Mn2+ or Mg2+
additional information
-
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
-
RNases H act as dimers, with two Mg2+ or other divalent cations being essential for correct protein structure, stability and enzyme activity
additional information
no activation by Ca2+, Zn2+, Ba2+, Ni2+, Cu2+, Fe2+, and Sr2+
additional information
-
type 2 enzyme requires divalent cations
additional information
Tma-RNase HI prefers Mg2+ to Mn2+ for activity, and specifically loses most of the Mg2+-dependent activity on removal of the hybrid binding domain and 87% of it by the mutation at the hybrid binding domain. Activity profiles of different metals and salt concentrations
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(1R,3R,4R,5R,8S)-8-benzyloxy-1-benzyloxymethyl-5-benzyloxyamino-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5R,8S)-8-benzyloxy-1-benzyloxymethyl-5-trifluoroacetamino-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-((methylthio)thiocarbonyl)oxy-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-(4-methylbenzoyl)-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-hydroxy-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane (20a) and (1R,3R,4R,5R,8S)-8-benzyloxy-1-benzyloxymethyl-5-hydroxy-3-(thymin-1-yl)-2-oxabicyclo[3.2.1]octane
-
-
(1R,3R,4R,5S,8S)-8-benzyloxy-1-benzyloxymethyl-5-methoxalyloxy-5-methyl-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,8S)-8-benzyloxy-1-benzyloxymethyl-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
(1R,3R,4R,8S)-8-benzyloxy-1-benzyloxymethyl-5-one-3-(thymin-1-yl)-2-oxa-bicyclo[3.2.1]octane
-
-
1,10-phenanthroline
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
1,6-dihydroxy-4-methyl-5-(N-phenoxyethanimidoyl)pyridin-2(1H)-one
1,6-dihydroxy-4-methyl-5-[N-[(4-methylphenyl)methoxy]ethanimidoyl]pyridin-2(1H)-one
-
-
1,6-dihydroxy-5-[N-[(2-methoxyphenyl)methoxy]ethanimidoyl]-4-methylpyridin-2(1H)-one
1,6-dihydroxy-5-[N-[(4-methoxyphenyl)methoxy]ethanimidoyl]-4-methylpyridin-2(1H)-one
1-(2-O-acetyl-3,5-O-benzyl-4-C-cyanoethyl-beta-D-ribofuranosyl)-thymine
-
-
1-(3,5-O-benzyl-2-O-phenoxythiocarbonyl-4-C-propionaldehyde-beta-D-ribofuranosyl)thymineO-benzyloxime
-
-
1-(3,5-O-benzyl-4-C-cyanoethyl-2-O-hydroxyl-beta-D-ribofuranosyl)-thymine
-
-
1-(3,5-O-benzyl-4-C-propionaldehyde-2-O-hydroxyl-beta-D-ribofuranosyl)thymine O-benzyl oxime
-
-
2-(2,3-dimethylphenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
-
2-(2,5-dimethylphenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
-
2-(4,6-dimethyl-3-oxo-1,2-benzothiazol-2(3H)-yl)-N-propylacetamide
-
-
2-(4-chlorophenyl)-6-fluoro-1,2-benzothiazol-3(2H)-one
-
-
2-(6-fluoro-3-oxo-1,2-benzothiazol-2(3H)-yl)-N-(4-methylphenyl)acetamide
-
-
2-phenyl-1,2-benzothiazol-3(2H)-one
-
-
2-[(cyclopentylcarbonyl)amino]-4-ethyl-5-methylthiophene-3-carboxamide
-
-
3,5-di-O-benzyl-4-C-cyanoethyl-1,2-O-isopropylidene-alpha-D-ribofuranose
-
-
4-[(4'-aminomethyl-1,1'-biphenyl)methyl]-1-hydroxy-1,8-naphthyridin-2-one
-
5-nitrofuran-2-carboxylic acid [[4-(4-bromophenyl)-thiazol-2-yl]-(tetrahydrofuran-2-ylmethyl)-carbamoyl]-methyl ester
-
derivative of 5-nitrofuran-2-carboxylic acid carbamoyl methyl ester. 20-25 microM effectively inhibit HIV-1 replication
5-[N-(4-fluorophenoxy)ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
5-[N-(benzyloxy)ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
-
5-[N-[(2-aminophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
5-[N-[(2-fluorophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
5-[N-[(4-fluorophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
6-(naphthalen-2-yl)-3-(pyridin-3-yl)[1,2,4]triazolo[3,4-b][1,3,4]thiadiazole
-
-
6-fluoro-2-(2-methylphenyl)-1,2-benzothiazol-3(2H)-one
-
-
6-fluoro-2-(4-methylphenyl)-1,2-benzothiazol-3(2H)-one
-
-
7-(furan-2-yl)-2-hydroxy-isoquinoline-1,3(2H,4H)-dione
YLC2-155
acetonitrile
-
20%, 50% loss of activity
alpha-hydroxytropolones
-
-
antisense oligodeoxynucleotides
-
directed against RNA polymerase II, replication protein A, and Ha-ras, determination of response in expression levels of the enzyme type 1 and 2, overview
-
Cu2+
-
in presence of Mg2+, inhibition
diphosphate
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
DNA
-
single-stranded or double-stranded, very strong
ethyl 6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxylate
Fe2+
-
in presence of Mg2+, inhibition
methyl 7-benzamido-2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinoline-4-carboxylate
-
Mg2+
-
Mg2+ is inhibitory at concentrations above 10 mM
mtSSB
repressive effect of mtSSB, mildly at 20 nM, strongly at 120 nM
-
N-(4-chlorophenyl)-6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide
-
-
N-(4-fluorophenyl)-6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide
-
-
N-(5-benzyl-1,3,4-thiadiazol-2-yl)-2-ethylhexanamide
-
-
N-benzyl-2-(6-fluoro-3-oxo-1,2-benzothiazol-2(3H)-yl)acetamide
-
-
N-cyclopentyl-2-(4,6-dimethyl-3-oxo[1,2]thiazolo[5,4-b]pyridin-2(3H)-yl)acetamide
-
-
N-cyclopropyl-1-methyl-3-oxo-1,3-dihydro-2,1-benzothiazole-5-sulfonamide
-
-
N-ethylmaleimide
-
inhibits wild-type enzyme and deletion mutant H1[DELTA1-73]
N-hydroxyisoquinolinedione
-
N-hydroxyisoquinolinediones
-
-
N-hydroxypyridinediones
-
-
N-[(4-fluorophenyl)methyl]-2,6-dihydroxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide
-
-
NaF
-
inhibition of Mg2+-dependent enzyme
NH4Cl
-
activity of enzyme form H1 decreases rapidly above 50 mM and becomes nearly abolished at 150 mM
Nucleic acids
-
enzyme form H1 is more susceptible to inhibition than enzyme form H2
-
poly(rA)
-
noncompetitive
-
poly(rArU)
-
noncompetitive
-
poly(rCdG)
-
uncompetitive
-
poly(rIdC)
-
competitive
-
Polyribonucleotides
-
slight
reovirus RNA
-
competitive
-
S-adenosylhomocysteine
-
-
SDS
-
0.002%, 50% loss of activity
spermidine
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
spermine
-
inhibition of Mn2+-dependent enzyme, no inhibition of the Mg2+-dependent enzyme
trihydroxy benzoyl biphenyl carboxylate hydrazone
BHMP07
trihydroxybenzoyl naphthyl hydrazone
-
Zn2+
-
in presence of Mg2+, inhibition
(NH4)2SO4
-
200 mM, 80% inhibition of Mn2+-dependent enzyme
(NH4)2SO4
-
complete inhibition at 100 mM, in presence of 10 mM MgCl2
(NH4)2SO4
-
isoenzyme II, 80% inhibition at 200 mM
1,6-dihydroxy-4-methyl-5-(N-phenoxyethanimidoyl)pyridin-2(1H)-one
-
-
1,6-dihydroxy-4-methyl-5-(N-phenoxyethanimidoyl)pyridin-2(1H)-one
-
1,6-dihydroxy-5-[N-[(2-methoxyphenyl)methoxy]ethanimidoyl]-4-methylpyridin-2(1H)-one
-
-
1,6-dihydroxy-5-[N-[(2-methoxyphenyl)methoxy]ethanimidoyl]-4-methylpyridin-2(1H)-one
-
1,6-dihydroxy-5-[N-[(4-methoxyphenyl)methoxy]ethanimidoyl]-4-methylpyridin-2(1H)-one
-
-
1,6-dihydroxy-5-[N-[(4-methoxyphenyl)methoxy]ethanimidoyl]-4-methylpyridin-2(1H)-one
-
5-[N-(4-fluorophenoxy)ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
-
5-[N-(4-fluorophenoxy)ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
5-[N-[(2-aminophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
-
5-[N-[(2-aminophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
5-[N-[(2-fluorophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
-
5-[N-[(2-fluorophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
5-[N-[(4-fluorophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
-
5-[N-[(4-fluorophenyl)methoxy]ethanimidoyl]-1,6-dihydroxy-4-methylpyridin-2(1H)-one
-
alpha-thujaplicin
-
i.e. 2-hydroxy-3-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
alpha-thujaplicin
-
i.e. 2-hydroxy-3-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
beta-thujaplicin
-
i.e. 2-hydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
beta-thujaplicin
-
i.e. 2-hydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
beta-thujaplicinol
-
i.e. 2,7-dihydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
beta-thujaplicinol
-
i.e. 2,7-dihydroxy-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
Ca2+
-
Ca2+
calcium ions generally inactivate the enzyme and abolish catalysis
Ca2+
Halalkalibacterium halodurans
-
Ca2+ substitution of either of the two active-site Mg2+ ions substantially increases the height of the reaction barrier and thereby abolishes the catalytic activity
Ca2+
-
calcium ions generally inactivate the enzyme and abolish catalysis
Ca2+
-
calcium ions generally inactivate the enzyme and abolish catalysis
Ca2+
-
calcium ions generally inactivate the enzyme and abolish catalysis
Co2+
over 95% inhibition at 5 mM and below
Co2+
-
in presence of Mg2+, inhibition
Dextran
-
-
Dextran
-
inhibits degradation of poly(rA)*poly(dT), no inhibition of degradation by phi174DNA-RNA. Dextran does not interfere with the recognition site, but rather blocks hydrolysis
ethyl 6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxylate
-
-
ethyl 6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxylate
-
gamma-thujaplicin
-
i.e. 2-hydroxy-5-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
gamma-thujaplicin
-
i.e. 2-hydroxy-5-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
KCl
-
activates by 50% at 50 mM, inhibits by 90% at 200 mM
KCl
-
half-maximal inhibition at 150 mM
KCl
-
enzyme form HA1, HA2, and HB1
KCl
-
activity of enzyme form H1 decreases rapidly above 50 mM and becomes nearly abolished at 150 mM
manicol
-
i.e. 1,2,3,4-tetrahydro-2,7-dihydroxy-9-methyl-2-(1-methylethyl)-6H-benzocyclohepten-6-one
manicol
-
i.e. 1,2,3,4-tetrahydro-2,7-dihydroxy-9-methyl-2-(1-methylethyl)-6H-benzocyclohepten-6-one
Mn2+
wild-type enzyme, above 0.1 mM, activating below, activating metal ion binding site is site 1, inhibitory binding site is site 2
Mn2+
40% inhibition at 100 mM
Mn2+
-
in presence of Mg2+, strong inhibition
Mn2+
-
Mn2+ inhibition of in vitro reverse transcriptase activity is greatly reduced in all the suppressor mutants, whereas RNAse H activity and cleavage specificity remain largely unchanged
Mn2+
-
the activity of wild-type protein is stimulated by Mn2+, whereas this cation significantly inhibits the activity of C-terminal truncated mutant proteins
Mn2+
-
can substitute for Mg2+, activates N-terminally truncated mutant RNHIDELTA47 and inhibits the full length enzyme dependent on the presence of the N-terminal 47 amino acids
NaCl
-
activates by 50% at 50 mM, inhibits by 90% at 200 mM
NaCl
-
activity of enzyme form H1 decreases rapidly above 50 mM and becomes nearly abolished at 150 mM
NEM
-
-
NEM
-
the Mg2+-dependent activity is inhibited by 60% at 20 mM. The Mn2+-dependent activity is unaffected
NEM
-
2 mM, 80% inhibition of Mn2+-dependent enzyme, complete inhibition of Mg2+-dependent enzyme
NEM
-
2 mM, 50% inhibition
NEM
-
enzyme form H2. No effect on enzyme form H1
NEM
-
Mn2+-dependent activity is moderately sensitive, even at high concentrations
NEM
-
0.03 mM, 50% inhibition after 30 min
NEM
-
Mg2+-dependent activity is highly sensitive
Ni2+
nearly complete inhibition at 5 mM and below
nootkatin
-
i.e. 2-hydroxy-5-(3-methyl-2-butenyl)-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one, slight inhibition
nootkatin
-
i.e. 2-hydroxy-5-(3-methyl-2-butenyl)-4-(1-methylethyl)-2,4,6-cycloheptatrien-1-one
PCMB
-
-
PCMB
-
2 mM, complete inhibition of Mn2+-dependent enzyme and Mg2+-dependent enzyme
PCMB
-
in absence of 2-mercaptoethanol
PCMB
-
in absence of 2-mercaptoethanol, isoenzyme I and III are completely inhibited by 0.2 mM PCMB, Activity of isoenzyme II is inhibited 20%
rifampicin
-
derivatives
rifampicin
-
and some derivatives
S-adenosylmethionine
-
-
S-adenosylmethionine
-
at 35°C but not at 0°C
S-adenosylmethionine
-
2 mM or above
tropolone
-
i.e. 2-hydroxy-2,4,6-cycloheptatrien-1-one, slight inhibition
tropolone
-
i.e. 2-hydroxy-2,4,6-cycloheptatrien-1-one
additional information
-
selectivity of tropolone derivatives for RNase H, IC50 values, inhibition mechanism, overview
-
additional information
-
inhibition of hepatitis B virus (HBV) replication by alpha-tropolone, N-hydroxyisoquinolinedione, and N-hydroxypyridinedione ribonuclease H inhibitors. Three compound classes, the alpha-hydroxytropolones, N-hydroxyisoquinolinediones, and N-hydroxypyridinediones are found by inhibitor screening, that suppress viral replication in cells by blocking the HBV RNaseH. These compounds preferentially suppress the plus-polarity DNA strands, induce truncation of the minus-polarity DNA strands, and cause accumulation of extensive RNA:DNA heteroduplexes in capsids as expected from their inhibition of the RNaseH. Seven N-hydroxyisoquinolinediones inhibit HBV replication, but the therapeutic indexes does not improve over what was reported. All nine of the N-hydroxypyridinedioness inhibit HBV replication. The N-hydroxypyridinedione compound class holds potential for antiviral discovery. No inhibition by 7-benzamido-N,N-diethyl-2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide and methyl 7-benzamido-2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinoline-4-carboxylate. Determination of cellular toxicity and EC50 values for HBV replication inhibition in presence of DNA for the inhibitor compounds, overview. Comparison with effects on the human enzyme
-
additional information
-
presence of intrinsic cell-type specific factors affecting the activity and localization of type 2 enzyme
-
additional information
-
selectivity of tropolone derivatives for RNase H, IC50 values, inhibition mechanism, overview
-
additional information
-
chimeric substrates containing 2'-methoxyethyl nucleotides inhibit human RNase H1 activity
-
additional information
-
drug design and synthesis by 2',4'-propylene-bridged thymidine, and five 8'-Me/NH2/OH variants thereof, introduction into 15mer oligodeoxynucleotides, the compounds inhibit the enzyme by formation of stable complexes with RNA, inhibitory effect of the variants, overview
-
additional information
for screening of inhibitors, a label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology is used, overview
-
additional information
alpha-tropolone, N-hydroxyisoquinolinedione, and N-hydroxypyridinedione ribonuclease H inhibitors are tested against human RNase H compared to hepatitis B virus RNase H. Replication inhibition efficacy and cytotoxicity, overview. No or poor inhibition by 7-benzamido-N,N-diethyl-2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide, 1,6-dihydroxy-4-methyl-5-[N-[(4-methylphenyl)methoxy]ethanimidoyl]pyridin-2(1H)-one, N-(4-fluorophenyl)-6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide, N-[(4-fluorophenyl)methyl]-2,6-dihydroxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide, and N-(4-chlorophenyl)-6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide
-
additional information
-
alpha-tropolone, N-hydroxyisoquinolinedione, and N-hydroxypyridinedione ribonuclease H inhibitors are tested against human RNase H compared to hepatitis B virus RNase H. Replication inhibition efficacy and cytotoxicity, overview. No or poor inhibition by 7-benzamido-N,N-diethyl-2-hydroxy-1,3-dioxo-1,2,3,4-tetrahydroisoquinoline-4-carboxamide, 1,6-dihydroxy-4-methyl-5-[N-[(4-methylphenyl)methoxy]ethanimidoyl]pyridin-2(1H)-one, N-(4-fluorophenyl)-6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide, N-[(4-fluorophenyl)methyl]-2,6-dihydroxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide, and N-(4-chlorophenyl)-6-hydroxy-2-methoxy-5,7-dioxo-5,6,7,8-tetrahydro-1,6-naphthyridine-8-carboxamide
-
additional information
5'-boronic acid modified oligonucleotides (ORNs) hybridized to a RNA target sequence convert RNase H into an inactivated enzyme complex. The dynamic formation of a boronate ester upon addition of a diol moiety disrupts the enzyme-inhibitor complex and reactivates RNase H. Reactivation of RNase H function can also be engineered through short RNA trimers inputs that fashion RNase H from a non-specific DNA-guided enzyme into an informational and programmable RNA-guided one. Programmable RNA recognition and cleavage, method, overview
-
additional information
-
a 5' RNA flap Okazaki fragment intermediate impairs PabRNase HII endonuclease activity. Introduction of mismatches into the RNA portion near the RNA-DNA junction decreases both the specificity and the efficiency of cleavage by PabRNase HII
-
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evolution
-
reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
evolution
-
reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
evolution
reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
evolution
Halalkalibacterium halodurans
ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and is a prototypical member of a large family of enzymes that use two-metal ion (Mg2+ or Mn2+) catalysis to cleave nucleic acids
evolution
-
RNaseH enzymes belong to the nucleotidyl transferase superfamily whose members share a similar protein fold and catalytic mechanism
evolution
-
the reverse transcriptase (RT) and ribonuclease H are among the most ancient and abundant protein folds. RNases H may have evolved from ribozymes, related to viroids, early in the RNA world, forming ribosomes, RNA replicases and polymerases. Basic RNA-binding peptides enhance ribozyme catalysis. RT and ribozymes or RNases H are present today in bacterial group II introns, the precedents of transposable elements. Thousands of unique RTs and RNases H are present in eukaryotes, bacteria, and viruses
malfunction
mutations in each of the three RNase H2 subunits are implicated in a human auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
malfunction
-
strains deficient in RNase H2 display a weak mutator phenotype which is consistent with a defect in DNA repair. RNase H2 defects cause alterations in the timing of cell cycle transitions
malfunction
deletion of rnhB sensitizes Mycobacterium smegmatis to UV irradiation in stationary phase. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
malfunction
DELTArnhA and DELTArnhC are synthetically lethal
malfunction
DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
malfunction
disease-causing mutations impairs the process of RNase H1 direction of origin-specific initiation of DNA replication in human mitochondria. Depletion of RNase H1 causes a reduction in mtDNA level. In an RNase H1-deficient patient cell line, the precise initiation of mtDNA replication is lost and DNA synthesis is initiated from multiple sites throughout the mitochondrial control region. Impaired RNase H1 activity changes replication initiation in vivo. Effects of disease causing mutations in RNASEH1, which are associated with adult-onset mitochondrial encephalomyopathy, phenotype and mechanism, overview
malfunction
disrupting the activity of the two enzymes RNase H1 and H2 (rnh1DELTA rnh201DELTA in Saccharomyces cerevisiae) is a useful tool for increasing the persistence of DNA:RNA hybrids and studying the effects of hybrid-induced instability. In the absence of RNase H activity, the levels of hybrids formed at susceptible loci increase dramatically. This increase in hybrids is associated with increased rates of genome instability that include loss of heterozygosity (LOH) events, loss of entire chromosomes, and recombination at the ribosomal locus. rnh1DELTA rnh201DELTA mutants display an increase in Rad52-GFP foci. Cells lacking RNase H1 and H2 have a larger fraction of persistent R-loop induced damage than wild-type cells or cells lacking only one of the RNases H, failure to observe accumulating foci early in the cell cycle, phenotype, overview
malfunction
disruption of the rnhA gene has been reported to increase a basal level of SOS expression in Escherichia coli, probably due to persistence of R-loops on the chromosome
malfunction
-
inhibition of hepatitis B virus (HBV) replication by N-hydroxyisoquinolinedione and N-hydroxypyridinedione ribonuclease H inhibitors. Blocking the HBV RNaseH activity prevents removal of the RNA strand from the minus-polarity DNA strand, resulting in an accumulation of RNA:DNA heteroduplexes
malfunction
-
mice deficient in RNase H1 that localizes to mitochondria die during embryogenesis, probably due to the defective processing of R-loops. RNase H2 knockout mice are also not viable, and mutations in either of the human genes can cause Aicardi-Goutieres Syndrome, a severe inheritable neurodevelopmental disorder. In this disease, uncleaved RNA-DNA hybrids accumulate within cells that possibly upregulate interferon via the nucleic acid sensor cyclic GMP-AMP synthase (cGAS) and its adaptor protein STING
malfunction
pathogenic consequences of disease causing mutations in RNase H1, overview. Loss of RNase H1 leads to primer retention at both OriH and OriL. RNase H1 mutations associated with mtDNA replication defects are identified in patients with mitochondrial encephalomyopathy. In vitro, the mutant proteins V142I, A185V, and R157stop have reduced activity on RNA-DNA hybrids. Analysis of patient samples show lower mtDNA levels and increased replication stalling. The disease causing mutations disrupt the conformational stability of RNase H1. RNase H1 mutations impair primer removal at OriL in vivo. The potential structural/functional consequences of the V142I and A185V mutations are assessed by looking at the crystal structure of wild-type RNase H1, PDB ID 2QK9. Both residues are located near the active site
malfunction
-
RNase H2 and H1 knockout mutations in either of the human genes can cause Aicardi-Goutieres Syndrome, a severe inheritable neurodevelopmental disorder. In this disease, uncleaved RNA-DNA hybrids accumulate within cells that possibly upregulate interferon via the nucleic acid sensor cyclic GMP-AMP synthase (cGAS) and its adaptor protein STING
malfunction
strains with both flap endonuclease (Fen1) and RNase HII deleted grow well. GINS-associated nuclease, GAN, activity is therefore sufficient for viability in the absence of both RNase HII and Fen1, but it is not possible to construct a strain with both RNase HII and GAN deleted. Fen1 alone is therefore insufficient for viability in the absence of both RNase HII and GAN. Deletion of both Fen1 and GAN or of both RNase HII and GAN is lethal
malfunction
-
DELTArnhA and DELTArnhC are synthetically lethal
-
malfunction
-
deletion of rnhB sensitizes Mycobacterium smegmatis to UV irradiation in stationary phase. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
-
malfunction
-
DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
-
malfunction
-
DELTArnhA and DELTArnhC are synthetically lethal
-
malfunction
-
deletion of rnhB sensitizes Mycobacterium smegmatis to UV irradiation in stationary phase. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
-
malfunction
-
DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide
-
metabolism
a two-nuclease pathway involving RNase H1 is required for primer removal at human mitochondrial OriL
metabolism
RNase H1 involvement in mtDNA synthesis, detailed overview. RNase H1 is involved in primer processing in human mitochondria
metabolism
the degradation of cleaved mRNA fragments by RNase H1-dependent ASOs involves XRN1, a cytoplasm-localized exonuclease, whereas the degradation of cleavage fragments of nuclear RNAs largely depend on XRN2, a nuclear-localized exonuclease
physiological function
ribonuclease H2 is the major nuclear enzyme involved in the degradation of RNA/DNA hybrids and removal of ribonucleotides misincorporated in genomic DNA
physiological function
-
RNase H1 is an indispensable protein for Okazaki fragment processing in human mtDNA replication
physiological function
-
RNase H2 cleaves RNA sequences that are part of RNA/DNA hybrids or that are incorporated into DNA, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces Aicardi-Goutieres syndrome, a severe autoimmune disorder
physiological function
RNase H2 junction recognition is important for the removal of RNA embedded in DNA and may play an important role in DNA replication and repair
physiological function
-
RNase HIII-type ribonucleases are members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are possibly be involved in DNA replication and repair
physiological function
-
both Pf-RNase HII and Pf-FEN-1 are required for the effective processing of an Okazaki substrate
physiological function
the enzyme is involved in RNA primer removal during DNA replication
physiological function
-
ribonucleotide excision repair is most efficient when the ribonucleotide is incised by RNase H2. RNase H1 fails to substitute for RNase H2 in the incision step of ribonucleotide excision repair
physiological function
-
RNase H is essential for foamy viral protease activity
physiological function
-
RNase H2 is implicated in the processing of the 5' ends of Okazaki fragments. RNase H2 also links DNA replication and DNA repair through ribonucleotide excision repair. The RNase H2 interaction network also functions to suppress genome instability
physiological function
-
RNase HI stimulates the activity of RnlA toxin
physiological function
-
DNA replication requires RNA primers to initiate lagging strand DNA synthesis and their subsequent removal by the RNase. RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life
physiological function
R-loops are structures that form when RNA invades double-stranded DNA and hybridizes to complementary genomic sequences. R-loops can form spontaneously across many genomic loci, but the activity of two endogenous RNases H prevents their accumulation and persistence. RNase H enables efficient repair of R-loop induced DNA damage. RNase H1 and H2 are highly conserved ribonucleases with the ability to degrade the RNA moiety of a DNA:RNA hybrid. The RNases H are important protectors of genome stability, mechanisms, overview. The presence of either RNase H1 or H2 prevents the accumulation of DNA damage in G2-M
physiological function
ribonuclease H (RNase H) is an endoribonuclease that specifically cleaves the RNA strand of RNA/DNA hybrids1. It cleaves the PO-3' bond of the substrate with a two-metal-ion catalysis mechanism, in which two divalent cations, such as Mg2+ and Mn2+, directly participate in the catalytic function. Escherichia coli RNase H1 exhibits 3'-JRNase activity for dsDNAR1 much more effectively in the presence of manganese ions than in the presence of magnesium ions, regardless of whether this substrate is cleaved by 5'-JRNase activity of Escherichia coli RNase H2 in advance or not, and can excise the single ribonucleotide in collaboration with Escherichia coli RNase H2. Not only RNase H2 but also RNase H1 is involved in the RER pathway. Role of RNase H1 in DNA repair: removal of single ribonucleotide misincorporated into DNA in collaboration with RNase H2. The 3'-JRNase activity of Escherichia coli RNase H1 may not be involved in SOS response, because this activity may not be required for R-loop resolution
physiological function
Halalkalibacterium halodurans
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ribonucleotides within RNA-DNA hybrids are recognized and hydrolyzed by the RNase H enzymes
physiological function
RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
physiological function
RNase H1 is required for mtDNA replication, it directs origin-specific initiation of DNA replication in human mitochondria. RNase H1 is required for R-loop processing, primer formation, and mtDNA maintenance in vivo. Both R-loop formation and DNA replication initiation are stimulated by the mitochondrial single-stranded DNA binding protein. In addition to the potential role in R-loop processing, RNase H1 has also been proposed to be involved in mitochondrial pre-rRNA processing by interacting with the mitochondrial protein P32, which slightly enhances the RNase H1 enzymatic activity
physiological function
RNase H1-dependent antisense oligonucleotides (ASOs) can direct RNase H1 cleavage of target RNAs. ASOs are robustly active in directing RNA cleavage in both the cytoplasm and the nucleus. ASOs are effective in reducing the levels of targeted small nuclear RNAs (snRNAs), small cajal body RNAs (scaRNAs), small nucleolar RNAs (snoRNAs), and nucleoplasmic long non-coding RNAs (lncRNAs) and premRNAs. In the cytoplasm, RNase H1 is enriched in the mitochondria, where it is involved in mitochondrial DNA replication and RNA processing, by removing the RNA/DNA hybrids during replication and transcription. Pre-existing cytoplasmic mRNAs can be cleaved by RNase H1-ASO treatment. RNase H1-dependent ASOs reduce cytoplasmic mRNAs much faster than normal mRNA decay
physiological function
RNase H1-dependent antisense oligonucleotides (ASOs) can recruit RNase H1 to cleave the RNA substrate within the region complementary to the DNA portion of ASOs. ASOs can degrade complementary RNAs in both the nucleus and the cytoplasm. Since cytoplasmic mRNAs are actively engaged in translation, ASO activity may thus be affected by translating ribosomes that scan the mRNAs. mRNAs associated with ribosomes can be cleaved using ASOs and that translation can alter ASO activity. Translation inhibition tends to increase ASO activity when targeting the coding regions of efficiently translated mRNAs, but not nuclear non-coding RNAs or less efficiently translated mRNAs. Increasing the level of RNase H1 protein eliminates the enhancing effects of translation inhibition on ASO activity, suggesting that RNase H1 recruitment to ASO/mRNA heteroduplexes is a rate limiting step and that translating ribosomes can inhibit RNase H1 recruitment. Consistently, ASO activity is not increased by translation inhibition when targeting the 3' UTRs, independent of the translation efficiency of the mRNAs. Contrarily, the activity of 3' UTR-targeting ASOs tends to be reduced upon translation inhibition, likely due to decreased accessibility. Overexpression of RNaseH1 attenuates the enhancement in ASO activity by CHX treatment
physiological function
RNase HII is necessary for viability of Thermococcus kodakarensis. RNase HII is proposed to participate in primer processing during Okazaki fragment maturation. In Thermococcus kodakarensis, either flap endonuclease (Fen1) or GINS-associated nuclease (GAN) activity is sufficient for viability. GAN can support growth in the absence of both Fen1 and RNase HII, but Fen1 and RNase HII are required for viability in the absence of GAN. Individually, Fen1, GAN, and RNase HII are not essential for viability
physiological function
RnhA like RnhC is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
physiological function
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase. RnhC in pathogenic mycobacteria is a possible candidate drug discovery target for tuberculosis and leprosy
physiological function
-
the endonucleolytic RNaseH activity (EC 3.1.26.4) requires an DNA:RNA duplex 14 nt or more and cannot tolerate a stem-loop in either the RNA or DNA strands. It tolerates a nick in the DNA strand but not a gap. The RNaseH has no obvious sequence specificity or positional dependence within the RNA, and it cuts the RNA at multiple positions even within the minimal 14 nt duplex. The RNaseH also possesses a processive 3'-5' exoribonuclease activity (EC 3.1.13.2) that is slower than the endonucleolytic reaction. The HBV reverse transcription mechanism features an initial endoribonucleolytic cut, 3'-5' degradation of RNA, and a sequence-independent terminal RNA cleavage
physiological function
-
the endonucleolytic RNaseH activity (EC 3.1.26.4) requires an DNA:RNA duplex 14 nt or more and cannot tolerate a stem-loop in either the RNA or DNA strands. It tolerates a nick in the DNA strand but not a gap. The RNaseH has no obvious sequence specificity or positional dependence within the RNA, and it cuts the RNA at multiple positions even within the minimal 14 nt duplex. The RNaseH also possesses a processive 3'-5' exoribonuclease activity (EC 3.1.13.2) that is slower than the endonucleolytic reaction. The RNaseH is one of two enzymatically active domains on the HBV polymerase that synthesizes the partially double-stranded DNA genome via reverse transcription. The reverse transcriptase (RT) domain of the polymerase protein copies the pregenomic RNA (pgRNA) template to form the minus-polarity DNA strand. The RNaseH recognizes RNA:DNA heteroduplexes that are formed during minus-polarity DNA synthesis and degrades the RNA strand. The polymerase then synthesizes the positive polarity DNA strand, but it typically arrests after making only about 50% of the plus-polarity DNA strand. Both enzymatic activities of the polymerase are required for synthesis of the HBV genome
physiological function
-
the RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life
physiological function
the RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life
physiological function
-
the RNase H enzymes mediate viral and cellular replication and antiviral defense in eukaryotes and prokaryotes, splicing, R-loop resolvation, DNA repair. RNase H-like activities are also required for the activity of small regulatory RNAs. Virtually all known immune defense mechanisms against viruses, phages, transposable elements, and extracellular pathogens require RNase H-like enzymes. RNase H-like activities of retroviruses, transposable elements, and phages, have built up innate and adaptive immune systems throughout all domains of life. R-loops are formed when an RNA strand intercalates into dsDNA, resulting in RNA-DNA hybrids and single-stranded DNA loops. R-loops affect promoter activities, with a role in gene expression (e.g. of the c-Myc proto-oncogene), genome stability, CRISPR-Cas immunity, DNA repair, and cancer formation. RNases H can remove the RNA moiety and prevent deleterious DNA breaks
physiological function
the role of Ribonuclease H1 (RNase H1) during primer removal and ligation at the mitochondrial origin of light-strand DNA synthesis (OriL) is a key step in mitochondrial DNA maintenance. FEN1 or an enzyme with FEN1-like activity is required for the last step of L-strand maturation before ligation. RNase H1 alone is insufficient for maturation of the nascent L-strand during DNA synthesis, the FEN1-like activity together with RNase H1 is needed for efficient ligation at OriL. But FEN1 is not able to substitute for RNase H1 during primer removal and L-strand maturation
physiological function
-
RNase HIII-type ribonucleases are members of the RNase H group of endonucleases which hydrolyze RNA from RNA/DNA hybrids and are possibly be involved in DNA replication and repair
-
physiological function
-
RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
-
physiological function
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase. RnhC in pathogenic mycobacteria is a possible candidate drug discovery target for tuberculosis and leprosy
-
physiological function
-
RnhA like RnhC is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
-
physiological function
-
RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
-
physiological function
-
RnhC like RnhA is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase. RnhC in pathogenic mycobacteria is a possible candidate drug discovery target for tuberculosis and leprosy
-
physiological function
-
RnhA like RnhC is an RNase H1-type magnesium-dependent endonuclease with stringent specificity for RNA:DNA hybrid duplexes. RNase H1 activity is essential for mycobacterial growth and can be provided by either RnhC or RnhA. The RNase H2 enzymes RnhB and RnhD are dispensable for growth. RnhB and RnhA collaborate to protect Mycobacterium smegmatis against oxidative damage in stationary phase
-
physiological function
Halalkalibacterium halodurans C-125
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ribonucleotides within RNA-DNA hybrids are recognized and hydrolyzed by the RNase H enzymes
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additional information
-
RNase H exists as a free enzyme
additional information
the C-terminal RNase H domain loses the ability to suppress the RNase H deficiency of an Escherichia coli rnhA mutant, the hybrid binding domain is responsible for in vivo RNase H activity
additional information
the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+. Residue Y163 is important for binding of both (5')RNA-DNA(3') junctions and RNA/DNA substrates
additional information
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the RNase HII contains a regulatory C-terminal tail. The C-terminus might form a short alpha-helix in which two residues, I195 and L196, are essential for the cleavage activity. The C-terminal alpha-helix is likely involved in the Mn2+-dependent substrate cleavage activity through stabilization of a flexible loop structure. Structure and function of both archaeal RNase HII, overview
additional information
the RNASEH2A C-terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer
additional information
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the RNASEH2A C-terminus is a eukaryotic adaptation for binding the two accessory subunits, with residues within it required for enzymatic activity. This C-terminal extension interacts with the RNASEH2C C terminus and both are necessary to form a stable, enzymatically active heterotrimer
additional information
the substrate binding site is located in the N-terminal TBP-like domain of RNase H3. The N-terminal domain of RNase H3 uses the flat surface of the b-sheet for substrate binding as TBP to bind DNA. This domain may greatly change conformation upon substrate binding
additional information
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the substrate binding site is located in the N-terminal TBP-like domain of RNase H3. The N-terminal domain of RNase H3 uses the flat surface of the b-sheet for substrate binding as TBP to bind DNA. This domain may greatly change conformation upon substrate binding
additional information
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the type 2 RNase H is an Mg2+- and alkaline pH-dependent enzyme
additional information
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translation initiates at each of the two in-frame AUGs of the Rnaseh1 mRNA, with the longer form being imported into mitochondria, regulation mechanisms, modelling, overview
additional information
Ala185 is adjacent to the catalytically essential Glu186, which coordinates a catalytic Mg2+ ion and forms part of a hydrophobic pocket that mediates the stabilising interactions in the active site region
additional information
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Ala185 is adjacent to the catalytically essential Glu186, which coordinates a catalytic Mg2+ ion and forms part of a hydrophobic pocket that mediates the stabilising interactions in the active site region
additional information
Halalkalibacterium halodurans
atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme, overview. The beta1 strand of the protein interacts with the DNA-RNA hybrid. Long timescale molecular dynamics simulations are performed on the BhRNase H-DNA-RNA hybrid complex and the respective monomers, analysis of recognition mechanism, conformational preorganization, active site dynamics and energetics involved in the complex formation, overview. The active site region contains three aspartic acids (D10, D71 and D131) and two glutamic acids (E48 and E127) along with two Mg2+ ions and water molecules, active site dynamics. The ability of the DNA strand in the hybrid duplex to sample conformations corresponding to typical A- and B-type nucleic acids and the characteristic minor groove width seem to be crucial for efficient binding. Sugar moieties in certain positions interacting with the protein structure undergo notable conformational transitions. The water coordination and arrangement around the metal ions in active site region are quite stable, suggesting their important role in enzymatic catalysis. Key interactions located at the interface of enzyme-nucleic acid complex are responsible for its stability
additional information
Halalkalibacterium halodurans
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conformational changes induced by RNase H binding of RNA:DNA heteroduplexes, crystal structure analysis of a dodecameric nonpolypurine/polypyrimidine tract RNA-DNA duplex and of the same sequence bound to RNase H, overview. The structural changes to the duplex include widening of the major groove to 12.5 A from 4.2 A and decrease in the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H
additional information
enzyme EcRNH has an active site centered on a putative DDEED motif inxadstead of DEDD conserved in other species
additional information
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enzyme EcRNH has an active site centered on a putative DDEED motif inxadstead of DEDD conserved in other species
additional information
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the RNaseH active site contains four conserved carboxylates (the DEDD motif) that coordinate two divalent cations, usually Mg2+. The RNA cleavage mechanism requires both cations to promote a hydroxyl-mediated nucleophilic scission reaction
additional information
three-dimensional structure is solved, revealing a conserved protein architecture, the RNase H fold
additional information
Halalkalibacterium halodurans C-125
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conformational changes induced by RNase H binding of RNA:DNA heteroduplexes, crystal structure analysis of a dodecameric nonpolypurine/polypyrimidine tract RNA-DNA duplex and of the same sequence bound to RNase H, overview. The structural changes to the duplex include widening of the major groove to 12.5 A from 4.2 A and decrease in the degree of bending along the axis which may play a crucial role in the ribonucleotide recognition and cleavage mechanism within RNase H
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E194A
the mutant exhibits 20 and 35% of the Mg2+- and Mn2+-dependent activities of the wild type enzyme, respectively
E196A
the mutant shows 84.8% Mn2+-dependent and 63% Mg2+-dependent activities compared to the wild type enzyme
E198A
the mutant shows 76.1% Mn2+-dependent and 63% Mg2+-dependent activities compared to the wild type enzyme
Y45A
the mutant shows 47.8% Mn2+-dependent and 5.4% Mg2+-dependent activities compared to the wild type enzyme
D101N
mutation results in more than 95% decrease in activity compared to wild-type enzyme
D129A
Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 2.2fold higher than the wild-type value. The turnover number is 30% of the wild-type value
D129N
mutation results in about 75% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 70% of the wild-type value. The turnover number is 20% of the wild-type value
D167A
no loss of activity
D37A
mutation results in about 90% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 80% of the wild-type value. The turnover number is 5% of the wild-type value
D37N
mutation results in about 10% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 1.5fold higher than the wild-type value. The turnover number is 40% of the wild-type value
D6N
mutation results in more than 95% decrease in activity compared to wild-type enzyme
E7Q
mutation results in more than 95% decrease in activity compared to wild-type enzyme
K39A
mutation results in about 30% decrease in activity compared to wild-type enzyme
R188A
no loss of activity
R45A
mutation results in about 5% decrease in activity compared to wild-type enzyme
S38A
mutation results in about 35% decrease in activity compared to wild-type enzyme
C33A/C63A/C133A
cysteine-free mutant, crystallization data
I53A
-
site-directed mutagenesis
I53D
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site-directed mutagenesis
L56A
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site-directed mutagenesis
L56D
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site-directed mutagenesis
L56S
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site-directed mutagenesis
C13A/C63A/C133A/E135C
-
site-directed mutagenesis, 37% activity compared to the wild-type enzyme
D10A/I53D
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mutations simultaneously destabilize the core and stabilize the periphery of the protein. Comparison with stabilized mutant D10A, reference protein for two-state folding
D10N
site-directed mutagenesis, active site mutant, 1700fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
D134A
site-directed mutagenesis, mutant shows activity in presence of Mn2+, activity is similar to the wild-type enzyme, but the mutant is not inhibited by Mn2+ concentrations above 0.1 mM in contrast to the wild-type enzyme, 5.0fold increased dissociation constants for binding of Mn2+
D134A/L87A
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site-directed mutagenesis, crystal structure analysis with bound Mn2+
D134N
site-directed mutagenesis, mutant shows high activity in presence of Mn2+ without inhibition at higher Mn2+ concentrations, and 5.4fold increased dissociation constants for binding of Mn2+
D70N
site-directed mutagenesis, active site mutant, 440fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
E48A
site-directed mutagenesis, mutant shows activity in presence of Mn2+, activity is similar to the wild-type enzyme, but the mutant is not inhibited by Mn2+ concentrations above 0.1 mM in contrast to the wild-type enzyme, 10fold increased dissociation constants for binding of Mn2+
E48A/D134A
site-directed mutagenesis, active site mutant, highly reduced activity and 65fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
E48A/D134N
site-directed mutagenesis, active site mutant, reduced activity and 260fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
E48A/L87A
-
site-directed mutagenesis, crystal structure analysis with bound Mn2+
E48A/L87A/D134A
-
site-directed mutagenesis, crystal structure analysis with bound Mn2+
E48Q
site-directed mutagenesis, mutant shows activity in presence of Mn2+ and 9.2fold increased dissociation constants for binding of Mn2+ compared to the wild-type enzyme
I25A
large destabilization, compared to wild-type. Mutant is active and retains a native-like fold. Mutation results in the equilibrium population of the folding intermediate under near-native conditions. The intermediate is undetectable in a series of heteronuclear single quantum coherences, revealing the dynamic nature of this partially unfolded form on the timescale of NMR detection
E232A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
K50A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
L52A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Q54A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
S48A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
V42A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
Y46A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
E188A
Halalkalibacterium halodurans
site-directed mutagenesis, crystal structure analysis of the mutant bound to divalent metal ions
D702A/E731A
-
sequences encoding HBV RNaseH residues 809-844 are deleted from pMal-HRHgtC to create pMal-HRHgtCDELTA5. Active site residues D702 and E731 are mutated to alanines to create pMAL-HRHgtC(D702A/E731A) which encodes an inactive RNaseH
D777A
-
the mutation in the RNase H domain of hepatitis B virus polymerase yields significantly reduced amounts of viral DNAs Minus-strand DNA synthesis is incomplete due to loss of catalytic activity of RNase H
R703A
-
the mutation in the RNase H domain of hepatitis B virus polymerase yields significantly reduced amounts of viral DNAs. Minus-strand DNA synthesis is incomplete due to loss of catalytic activity of RNase H
R781A
-
the mutation in the RNase H domain of hepatitis B virus polymerase yields significantly reduced amounts of viral DNAs. The minus-strand DNA synthesis is near complete to some extent, while the plus-strand DNA synthesis (i.e., relaxed circular DNA) is severely impaired due to the defect in RNase H activity
C147A
-
site-directed mutagenesis, mutant is active under reducing and oxidizing conditions
C147A/C148A
-
site-directed mutagenesis, mutant is active under reducing and oxidizing conditions
C148A
-
site-directed mutagenesis, mutant is active under reducing and oxidizing conditions
C191A
-
site-directed mutagenesis, mutant is active under reducing conditions, but shows poor activity under oxidizing conditions
D169A
active site residue mutation in subunit RNASEH2A
D2Y/L3P
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
D34A
active site residue mutation in subunit RNASEH2A
D39Y
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
F230L
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
G185V
mutation in subunit H2B associated with Aicardi-Goutieres' syndrome, near-normal activity
G83S
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
H264A
-
the mutation causes an about 100fold decrease in kcat under multiple-turnover conditions, but does not alter the Km value. The H264A mutant is not rescued by increasing the Mg2+ concentration to 80 mM
H86R
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K59A/K60A
-
site-directed mutagenesis in the hybrid binding domain, the mutation abolishes dsRNA binding
L138F
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
L60R
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P43H
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R108W
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R13H
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R186W
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R235Q
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R32A/R33A
-
site-directed mutagenesis in the hybrid binding domain outside of the interface, the mutation abolishes dsRNA binding
R35A
-
site-directed mutagenesis, the mutant shows a much lower specific activity than the wild-type enzyme
R57A
-
site-directed mutagenesis in the hybrid binding domain on the observed nucleic-acid interface, the mutation abolishes dsRNA binding
R72A/K73A
-
site-directed mutagenesis in the hybrid binding domain outside of the interface, the mutation abolishes dsRNA binding
S159I
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
S229P
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
T163I
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
T240M
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
V183M
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
V185G
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
W43A
-
site-directed mutagenesis in the hybrid binding domain on the observed nucleic-acid interface, the mutation abolishes dsRNA binding, the mutant shows a much lower specific activity than the wild-type enzyme
W73L
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
Y219H
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
Y29F
-
site-directed mutagenesis in the hybrid binding domain, the mutation abolishes dsRNA binding
D112N
-
site-directed mutagenesis, 0.17% activity compared to the wild-type enzyme, no Mn2+ binding
D149N
-
site-directed mutagenesis, 0.12% activity and slightly weakened Mn2+ binding properties compared to the wild-type enzyme
D7N
-
site-directed mutagenesis, 0.13% activity and slightly weakened Mn2+ binding properties compared to the wild-type enzyme
E8Q
-
site-directed mutagenesis, 0.14% activity and slightly weakened Mn2+ binding properties compared to the wild-type enzyme
D142N
mutation in strictly positionally conserved acidic residues, complete loss of activity
D170N
mutation in strictly positionally conserved acidic residues, complete loss of activity
D34N
mutation in strictly positionally conserved acidic residues, complete loss of activity
E35A
mutation in strictly positionally conserved acidic residues, complete loss of activity
G37S
mutation in subunit H2A identified in patients with Aicardi-Goutieres' syndrome. Mutation appears to distort the active site accounting for the demonstrated substrate specificity modification
D72N
site-directed mutagenesis, a conservative substitution at the metal binding site that abolishes the magnesium-dependent nuclease activity
E50Q
site-directed mutagenesis, a conservative substitution at the metal binding site that abolishes the magnesium-dependent nuclease activity
D72N
-
site-directed mutagenesis, a conservative substitution at the metal binding site that abolishes the magnesium-dependent nuclease activity
-
E50Q
-
site-directed mutagenesis, a conservative substitution at the metal binding site that abolishes the magnesium-dependent nuclease activity
-
D72N
-
site-directed mutagenesis, a conservative substitution at the metal binding site that abolishes the magnesium-dependent nuclease activity
-
E50Q
-
site-directed mutagenesis, a conservative substitution at the metal binding site that abolishes the magnesium-dependent nuclease activity
-
D110T
mutation causes loss of nuclease activity for the RNARNA duplex, nuclease activity for the RNA-DNA duplex substrate is similar to wild-type activity
G42S
-
the mutant shows strongly reduced activity compared to the wild type enzyme
I183M
-
site-directed mutagenesis in the polymerase domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
M520I
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
M520V
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
N398D
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
P45D/Y219A
-
the mutant shows strongly reduced activity compared to the wild type enzyme
S392C
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
S442P
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
S469G
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
T467A
-
site-directed mutagenesis in the connection domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
Y299C
-
site-directed mutagenesis in the RNase H domain, the mutation results in a Mn2+ suppressor mutant less sensitive to Mn2+ inhibition
D136H
stabilization in melting temperature by 9.7 degrees and 6.1 kJ per mol. 65% odf wild-type activity
N29K/D39G/M76V/K90N
stabilization in melting temperature by 18.7 degrees. 70% odf wild-type activity
N29K/D39G/M76V/K90N/R97G
stabilization in melting temperature by 22.1 degrees. 65% of wild-type activity
N29K/D39G/M76V/K90N/R97G/D136H
stabilization in melting temperature by 28.8 degrees. 43% of wild-type activity
R97G
stabilization in melting temperature by 5.4 degrees and 3.5 kJ per mol. 99% of wild-type activity
C58A/C145A
-
site-directed mutagenesis
D125N
mutation results in loss of dsRNase activity but not RNase H activity
D76N
no RNase H activity is detected
DELTAG144-T149
mutant enzyme lacking the C-terminal tail. The unfolding transition of the wild-type enzyme occurs much later than the mutant enzyme at high temperature
E52Q
no RNase H activity is detected
E8Q
-
site-directed mutagenesis
R118A
the specific activities of R118A-RNase HI for both 12-bp RNA/DNA and RNA/RNA substrates are reduced by approximately 10fold as compared to those of the wild-type protein
D125N
-
mutation results in loss of dsRNase activity but not RNase H activity
-
D76N
-
no RNase H activity is detected
-
D7N
-
enzyme loses RNase H activity and dsRNase activity in the presence of MnCl2
-
DELTAG144-T149
-
mutant enzyme lacking the C-terminal tail. The unfolding transition of the wild-type enzyme occurs much later than the mutant enzyme at high temperature
-
E52Q
-
no RNase H activity is detected
-
R118A
-
the specific activities of R118A-RNase HI for both 12-bp RNA/DNA and RNA/RNA substrates are reduced by approximately 10fold as compared to those of the wild-type protein
-
D105A
-
site-directed mutagenesis, nearly inactive mutant
D135A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
D7A
-
site-directed mutagenesis, nearly inactive mutant
E8A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
H132A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
D107N
site-directed mutagenesis, inactive mutant
G21S
site-directed mutagenesis, the mutation is located in the conserved GRG 2'-OH-sensing motif, the mutant has much lower activity on RNA/DNA and DNA-RNA/DNA in the presence of Mn2+. In the presence of Mg2+ it also shows reduced activity on substrates with (5')RNA-DNA(3') junction
R22A
site-directed mutagenesis, the R22A mutation does not alter Tm-RNase H2 activity on most substrates compared to the wild-type enzyme
Y163F
site-directed mutagenesis, Y163 is a key residue involved in 2'-OH binding, and its mutation to phenylalanine seriously reduces activity against all tested substrates
W22A
-
the mutation at the hybrid binding domain does not significantly affect the structure of enzyme. The pH, salt and metal ion dependencies of the mutant enzyme are similar to those of the wild-type enzyme. Its maximal Mn2+-dependent activity is also similar to that of wild-type enzyme. However, its maximal Mg2+-dependent activity is 7.5fold lower than that of the wild-type enzyme. The binding affinity of the mutant enzyme to the substrate is 21fold higher than that of the wild-type enzyme
-
A12S
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
A12S/K75M/A77P
-
site-directed mutagenesis, 40fold increased kcat/Km value compared to the wild-type enzyme, thermal stability similar to the wild-type enzyme
A77P
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
C13S/C63A/R135C
-
site-directed mutagenesis, 6.9% activity compared to the wild-type enzyme
C63A
-
site-directed mutagenesis, 94% activity compared to the wild-type enzyme
C63A/R135C
-
site-directed mutagenesis, 44% activity compared to the wild-type enzyme
D134H
-
site-directed mutagenesis, active site mutant, highly reduced catalytic activity
D134N
-
site-directed mutagenesis, active site mutant, similar to the wild-type enzyme
K75M
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
L56S
-
site-directed mutagenesis
A12S
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
-
A77P
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
-
D134N
-
site-directed mutagenesis, active site mutant, similar to the wild-type enzyme
-
K75M
-
random mutagenesis, roughly cumulative effect on enzyme activity, increased kcat/Km value compared to the wild-type enzyme
-
N159A
the mutant shows 20% and 2.6% activity in the presence of Mn2+ and Mg2+, respectively, compared to the wild type enzyme
N159D
the mutant shows 17% and 5.0% activity in the presence of Mg2+ and Mn2+, respectively, compared to the wild type enzyme
K143A
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
K143A
mutation results in about 80% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 31.3fold higher than the wild-type value. The turnover number is 150% of the wild-type value
R146A
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R146A
mutation results in more than 95% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 26.7fold higher than the wild-type value. The turnover number is 140% of the wild-type value
R46A
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
R46A
mutation results in about 50% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 60fold higher than the wild-type value. The turnover number is 130% of the wild-type value
S139A
no loss of activity
S139A
mutation results in about 40% decrease in activity compared to wild-type enzyme
Y164A
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
Y164A
mutation results in more than 95% decrease in activity compared to wild-type enzyme. Km-value for the 8-mer RNA-DNA/DNA hybrid substrate is 44.7fold higher than the wild-type value. The turnover number is 160% of the wild-type value
S94V
-
the mutation decreases the RNase H activity 3-6fold
S94V
-
the mutation decreases the RNase H activity 3-6fold
-
D10A
-
site-directed mutagenesis, active site mutant, no metal binding, altered folding kinetics in absence of metal ions to the values for wild-type enzyme in presence of metal ions
D10A
site-directed mutagenesis, active site mutant, poor binding of Mn2+
D10A
-
mutation relieves charge repulsion in the periphery of the protein and stabilizes the protein by more than 3 kcal/mol. Comparison with mutant D10A/I53D, reference protein for three-state folding
D202A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
D202A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
D97A
site-directed mutagenesis, inactive mutant
D97A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
E98A
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme
E98A
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
D132N
Halalkalibacterium halodurans
site-directed mutagenesis, crystal structure analysis of the mutant bound to divalent metal ions
D132N
Halalkalibacterium halodurans
perturbs the coordination shell of the A-site Mg2+
D132N
Halalkalibacterium halodurans
the plasmid expressing Bacillus halodurans RNase H
D192N
Halalkalibacterium halodurans
site-directed mutagenesis, crystal structure analysis of the mutant bound to divalent metal ions
D192N
Halalkalibacterium halodurans
crystallographic model. Although the mutant enzyme is completely inactive, D192N substitution supposedly does not significantly affect the active site architecture
A177T
mutation in subunit H2B associated with Aicardi-Goutieres' syndrome, near-normal activity
A177T
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
A177T
naturally occuring mutation in subunit RNASEH2B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS. The mutation disrupts the interface between a RNASEH2B alpha-helix and the RNASEH2C kinked helix
A185V
naturally occuring mutation of RNase H1, that is involved in adult-onset mitochondrial encephalomyopathy. Both RNase H1:V142I and RNase H1:A185V, alone or in combination, display impaired R-loop processing activity compared to wild-type RNase H1. As a consequence, the mutant RNase H1 proteins cannot support origin-specific initiation of DNA replication in vitro
A185V
site-directed mutagenesis, reconstruction of a disease causing mutation in RNaseH1 that impairs primer processing. Ala185 is adjacent to the catalytically essential Glu186, which coordinates a catalytic Mg2+ ion and forms part of a hydrophobic pocket that mediates the stabilising interactions in the active site region. The A185V mutation causes a steric clash in this pocket
G37S
mutation in subunit H2A associated with Aicardi-Goutieres' syndrome, greatly reduced activity and processivity
G37S
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K143I
mutation in subunit H2C associated with Aicardi-Goutieres' syndrome, near-normal activity
K143I
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K143I
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
K162T
mutation in subunit H2B associated with Aicardi-Goutieres' syndrome, near-normal activity
K162T
-
naturally occuring mutation in subunit B, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P138L
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P138L
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P151S
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P151S
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P76L
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
P76L
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R291H
-
naturally occuring mutation in subunit A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R291H
naturally occuring mutation in subunit RNASEH2A, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R69W
mutation in subunit H2C associated with Aicardi-Goutieres' syndrome, 30-40% of wild-type activity
R69W
-
naturally occuring mutation in subunit C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
R69W
naturally occuring mutation in subunit RNASEH2C, the mutation is involved in auto-inflammatory disorder, Aicardi-Goutieres syndrome, AGS
V142I
naturally occuring mutation of RNase H1, that is involved in adult-onset mitochondrial encephalomyopathy. Both RNase H1:V142I and RNase H1:A185V, alone or in combination, display impaired R-loop processing activity compared to wild-type RNase H1. As a consequence, the mutant RNase H1 proteins cannot support origin-specific initiation of DNA replication in vitro
V142I
site-directed mutagenesis, reconstruction of a disease causing mutation in RNaseH1 that impairs primer processing. Val142 stabilises the hydrophobic interface between helix alpha1 and sheet beta1. This interface is critical for proper alignment of Asp145 and Glu186 in catalysis which is likely disturbed in the V142I variant
A115E
partially enhanced nuclease activity for the RNA-DNA duplex substrate
A115E
mutation causes partially enhanced nuclease activity for the RNA-DNA duplex substrate, increase in its kcat of about 140%
F114E
reduced nuclease activity respectively for the RNA-DNA duplex substrate
F114E
mutations causes reduced nuclease activity for the RNA-DNA duplex substrate and reduced nuclease activity for the RNA-RNA duplex
R113E
partially reduced nuclease activity respectively for the RNA-DNA duplex substrate
R113E
mutations causes partially reduced nuclease activity for the RNA-DNA duplex substrate and reduced nuclease activity for the RNA-RNA duplex
D7N
-
site-directed mutagenesis
D7N
enzyme loses RNase H activity and dsRNase activity in the presence of MnCl2
W22A
site-directed mutagenesis, located in the hybrid binding domain
W22A
the mutation at the hybrid binding domain does not significantly affect the structure of enzyme. The pH, salt and metal ion dependencies of the mutant enzyme are similar to those of the wild-type enzyme. Its maximal Mn2+-dependent activity is also similar to that of wild-type enzyme. However, its maximal Mg2+-dependent activity is 7.5fold lower than that of the wild-type enzyme. The binding affinity of the mutant enzyme to the substrate is 21fold higher than that of the wild-type enzyme
additional information
of the highly conserved residues, mutations at Ser38, Lys39, Leu41, Arg45, Ser139, and Asp167 do not significantly affect the enzyme activity. Conversion of Asp6 to Asn, Glu7 to Gln, or Asp101 to Asn almost completely inactivated the enzyme, suggesting that these carboxylic acid groups of D6, E7, and D101 are essential for catalysis
additional information
-
of the highly conserved residues, mutations at Ser38, Lys39, Leu41, Arg45, Ser139, and Asp167 do not significantly affect the enzyme activity. Conversion of Asp6 to Asn, Glu7 to Gln, or Asp101 to Asn almost completely inactivated the enzyme, suggesting that these carboxylic acid groups of D6, E7, and D101 are essential for catalysis
additional information
-
Chlamydophila pneumoniae RNase HII can complement both Escherichia coli RNase HII and RNase HI, but Chlamydophila pneumoniae RNase HIII can only complement the latter
additional information
-
Chlamydophila pneumoniae RNase HII can complement both Escherichia coli RNase HII and RNase HI, but Chlamydophila pneumoniae RNase HIII can only complement the latter
-
additional information
-
construction of chimeric proteins of the Thermus thermophilus enzyme with the folding core of Chlorobium tepidum RNaseH, thermal stability analysis, overview
additional information
-
a Cys residue is substituted for Glu135 by site-directed mutagenesis in the mutant enzyme, in which all 3 free Cys residues are replaced by Ala and coupled with a maleimide group which is attached to the 5'-terminus of the nonadeoxyribonucleotide, 5'-GTCATCTCC-3', with a flexible tether. The resulting hybrid enzyme d9-C135/RNase H cleaves the phosphodiester bond between the fifth and sixth residues of the complementary nonaribonucleotide without addition of the oligodeoxyribonucleotide. The nonaribonucleotide is cleaved by the wild-type or unmodified mutant enzyme only when the complemetary oligoribonucleotide is present
additional information
-
a Cys residue is substituted for Glu135 by site-directed mutagenesis in the mutant enzyme, in which all 3 free Cys residues are replaced by Ala and coupled with a maleimide group which is attached to the 5'-terminus of the nonadeoxyribonucleotide, 5'-GTCATCTCC-3', with a flexible tether. The resulting hybrid enzyme d9-C135/RNase H shows site-specific cleavage of the 22-base RNA, 132-base RNA and 534-base RNA which contain a single target sequence, primarily at the unique phosphodiester bond within the target sequence. The hybrid enzyme performs multiple turnovers and at a substrate/enzyme ratio of 10:1 the RNAs are almost completely cleaved
additional information
-
all 3 Cys replaced with Ala, The recombinant enzyme is active and folds reversibly
additional information
-
construction of DNA-linked mutant enzyme, by cross-linking of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA, i.e. PPT-RNA, to the thiol group of Cys135 of the enzyme, mutant shows 4.2% activity compared to the wild-type enzyme
additional information
-
deletion of the basic loop in Escherichia coli RNase H inhibits but does not abolish activity. If the basic loop in Escherichia coli RNase H is inserted into an isolated inactive HIV-1 RNase H domain, Mn2+-dependent activity is partially restored
additional information
construction of deletion mutants of RNase HIII by truncation of the N-domain, residues 1-79, the C-domain, residues 80-310, the RNase HIIIDELTAC domain, residues 1-299, and C-domainDELTAC, residues 80-299, the mutant show reduced activity, overview
additional information
-
construction of deletion mutants of RNase HIII by truncation of the N-domain, residues 1-79, the C-domain, residues 80-310, the RNase HIIIDELTAC domain, residues 1-299, and C-domainDELTAC, residues 80-299, the mutant show reduced activity, overview
additional information
construction of mutant proteins of the intact protein and isolated N-domain, in which six of the seventeen residues corresponding to those involved in DNA binding of TBP are individually mutated to Ala. All of the mutants exhibit decreased enzymatic activities and/or substrate-binding affinities when compared to those of the parent proteins
additional information
-
construction of mutant proteins of the intact protein and isolated N-domain, in which six of the seventeen residues corresponding to those involved in DNA binding of TBP are individually mutated to Ala. All of the mutants exhibit decreased enzymatic activities and/or substrate-binding affinities when compared to those of the parent proteins
additional information
-
construction of deletion mutant H1[DELTA1-73]
additional information
-
full-length enzymes with defective HBDs indicates that this domain dramatically enhances both the specific activity and processivity of RNase H1
additional information
-
engineering of electrostatic and steric effects at the bottom of the minor groove for nuclease and thermodynamic stabilities and elicitation of RNase H, overview
additional information
-
knockdown of RNase H1, but neither of FEN1 nor DNA2, inhibits the recovery of mtDNA copy number
additional information
-
mapping of the positions of 29 mutations found in Aicardi-Goutieres syndrome patients, possible effects of these mutations on the protein stability and function, overview. Construction of deletion mutants AB14233C and ABDELTAPIPC, deletion mutant AB14-233C crystallizes more readily than the AB-PIPC and yields larger and regular crystals
additional information
the potential structural/functional consequences of the V142I and A185V mutations are assessed by looking at the crystal structure of wild type RNase H1, PDB ID 2QK9. Both residues are located near the active site. The disease causing mutations disrupt the conformational stability of RNase H1. RNase H1 mutations impair primer removal at OriL in vivo
additional information
-
the potential structural/functional consequences of the V142I and A185V mutations are assessed by looking at the crystal structure of wild type RNase H1, PDB ID 2QK9. Both residues are located near the active site. The disease causing mutations disrupt the conformational stability of RNase H1. RNase H1 mutations impair primer removal at OriL in vivo
additional information
lmo1273 can complement an Escherichia coli rnhA-rnhB thermosensitive growth phenotype, suggesting that it encodes a functional RNase H. DELTAlmo1273: Chromosomal deletion mutant. Inactivation of lmo1273 provokes a strong attenuation of virulence in the mouse model, and kinetic studies in infected mice reveals that multiplication of the lmo1273 mutant in target organs is significantly impaired. DELTAlmo1272/DELTA1273 double mutant. MIC2067-lmo1273 using the Escherichia coli strain MIC2067 (an rnhA-rnhB double mutant strain) and transformed it with plasmid pTrc99A-lmo1273, carrying the lmo1273 gene under IPTG-inducible promoter control
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fusion protein of maltose binding protein and the N-terminal RNase H domain shows RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein has additional CobC activity
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fusion protein of maltose binding protein and the N-terminal RNase H domain shows RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein has additional CobC activity
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fusion protein of maltose binding protein and the N-terminal RNase H domain shows RNase H activity with a hybrid RNA/DNA substrate as well as double-stranded RNase activity. The full-length protein has additional CobC activity
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deletion of gene rnhA, additional deletions of rnhB, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide, the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhA, additional deletions of rnhB, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide, the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhA, additional deletions of rnhB, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide, the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhB, additional deletions of rnhA, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide. The DELTArnhA/DELTArnhB double mutant is more sensitive than DELTArnhB to killing by UV in stationary phase, and the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhB, additional deletions of rnhA, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide. The DELTArnhA/DELTArnhB double mutant is more sensitive than DELTArnhB to killing by UV in stationary phase, and the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhB, additional deletions of rnhA, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide. The DELTArnhA/DELTArnhB double mutant is more sensitive than DELTArnhB to killing by UV in stationary phase, and the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhC, additional deletions of rnhB, rnhA, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal
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deletion of gene rnhC, additional deletions of rnhB, rnhA, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal
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deletion of gene rnhC, additional deletions of rnhB, rnhA, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal
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deletion of gene rnhD, additional deletions of rnhB, rnhC, and rnhA genes, genotyping of DELTArnh mutants and phenotypes, overview. The DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhD, additional deletions of rnhB, rnhC, and rnhA genes, genotyping of DELTArnh mutants and phenotypes, overview. The DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhD, additional deletions of rnhB, rnhC, and rnhA genes, genotyping of DELTArnh mutants and phenotypes, overview. The DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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deletion of gene rnhC, additional deletions of rnhB, rnhA, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal
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additional information
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deletion of gene rnhD, additional deletions of rnhB, rnhC, and rnhA genes, genotyping of DELTArnh mutants and phenotypes, overview. The DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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additional information
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deletion of gene rnhB, additional deletions of rnhA, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide. The DELTArnhA/DELTArnhB double mutant is more sensitive than DELTArnhB to killing by UV in stationary phase, and the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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additional information
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deletion of gene rnhA, additional deletions of rnhB, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide, the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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additional information
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deletion of gene rnhC, additional deletions of rnhB, rnhA, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal
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additional information
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deletion of gene rnhD, additional deletions of rnhB, rnhC, and rnhA genes, genotyping of DELTArnh mutants and phenotypes, overview. The DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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additional information
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deletion of gene rnhB, additional deletions of rnhA, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide. The DELTArnhA/DELTArnhB double mutant is more sensitive than DELTArnhB to killing by UV in stationary phase, and the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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additional information
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deletion of gene rnhA, additional deletions of rnhB, rnhC, and rnhD genes, genotyping of DELTArnh mutants and phenotypes, overview. DELTArnhA and DELTArnhC are synthetically lethal. DELTArnhA/DELTArnhB cells in stationary phase are sensitized to killing by hydrogen peroxide, the DELTArnhA/DELTArnhB/DELTArnhD mutant is about 17fold more sensitive than wild-type to killing in log phase by 20 mM H2O2
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construction of several deletion mutants
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generation of Ty1 reverse transcriptase/RNase H Mn2+ suppressor mutants capable of increased Ty1 transposition in pmr1DELTA cells for Mn2+ inhibition analysis, PMR1 codes for a P-type ATPase that regulates intracellular calcium and manganese ion homeostasis, and pmr1 mutants accumulate elevated intracellular manganese levels and display 100-fold less transposition than PMR1+ cells, suppressor point mutations localize not to the reverse transcriptase itself but to the RNase H domain of the protein, overview
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generation of the rnh1DELTA rnh201DELTA mutant with disrupted activity of the two enzymes RNase H1 and H, kinetics of foci persistence in rnh1D rnh201D cells, phenotype, overview. Cell cycle delay is observed in the rnh1DELTA rnh201DELTA strain and in rnh1DELTA rnh201DELTA TOP1-AID cells. The Rad52-GFP foci in the rnh1DELTA rnh201DELTA double mutant accumulated in a window that begins at the boundary between S and G2-M. Screen for suppressors of hybrid-induced lethality, identifying Pif1-E467G, this allele suppresses auxin sensitivity when introduced into rnh1DELTA rnh201DELTA TOP1-AID cells, indicating its responsibility for the suppression of lethality in the mutant cells. Pif1 mutants inhibit break-induced replication. RPA190 mutants allow for repair of R-loop induced damage. Rpa190-K1482T and -V1486F suppress auxin sensitivity of rnh1DELTA rnh201DELTA TOP1-AID cells
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generation of the rnh1DELTA rnh201DELTA mutant with disrupted activity of the two enzymes RNase H1 and H, kinetics of foci persistence in rnh1D rnh201D cells, phenotype, overview. Cell cycle delay is observed in the rnh1DELTA rnh201DELTA strain and in rnh1DELTA rnh201DELTA TOP1-AID cells. The Rad52-GFP foci in the rnh1DELTA rnh201DELTA double mutant accumulated in a window that begins at the boundary between S and G2-M. Screen for suppressors of hybrid-induced lethality, identifying Pif1-E467G, this allele suppresses auxin sensitivity when introduced into rnh1DELTA rnh201DELTA TOP1-AID cells, indicating its responsibility for the suppression of lethality in the mutant cells. Pif1 mutants inhibit break-induced replication. RPA190 mutants allow for repair of R-loop induced damage. Rpa190-K1482T and -V1486F suppress auxin sensitivity of rnh1DELTA rnh201DELTA TOP1-AID cells
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the Sto-RNase HI C-terminal residues, -IGCIILT, are introduced as a tag on three proteins. Each chimeric protein is more stable than its wild-type protein
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truncated mutant ST0519_1-195 retains only partial activity, while truncated mutant ST0519_1-196 completely loses its activity. Computational analysis of the substrate binding site through construction of diverse truncation mutants, overview
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construction of several truncation mutants, comprising residues 1-198, 1-203, 1-207, 1-213, or 1-217 of the wild-type enzyme, the truncated mutants' activities are increased or reduced compared to the wild-type enzyme, overview
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construction of a gene TK0805 deletion strain lacking RNase HII activity. The mutant strain shows reduced growth compared to wild-type
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construction of a gene TK0805 deletion strain lacking RNase HII activity. The mutant strain shows reduced growth compared to wild-type
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construction of a truncated mutant with 15 residues removed from the C-terminus
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the C-terminal RNase H domain loses the ability to suppress the RNase H deficiency of an Escherichia coli rnhA mutant. The substrate binding affinity of Tma-RNase HI is greatly reduced on removal of the hybrid binding domain or the mutation
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removal of the hybrid binding domain severely reduces the Mg2+-dependent activity of the enzyme by 750fold without significantly affecting the Mn2+-dependent activity
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removal of the hybrid binding domain severely reduces the Mg2+-dependent activity of the enzyme by 750fold without significantly affecting the Mn2+-dependent activity
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construction of DNA-linked mutant enzyme, by cross-linking of the 15mer DNA, which is complementary to the polypurine-tract sequence of human immunodeficiency virus-1 RNA, i.e. PPT-RNA, to the thiol group of Cys13 or Cys135 of the enzyme, mutants shows 0.69% activity compared to the wild-type enzyme
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isolation of a mutant enzyme with enhanced activity at moderate temperatures, genetic method development
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populating the folded region of the intermediate mimic by protein engineering
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populating the folded region of the intermediate mimic by protein engineering
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construction of chimeric proteins of the Thermus thermophilus enzyme with the folding core of Chlorobium tepidum RNaseH, thermal stability analysis, overview
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isolation of a mutant enzyme with enhanced activity at moderate temperatures, genetic method development
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construction of several N-terminally truncated enzyme forms for investigation of structure-function relationship
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