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Literature summary for 6.5.1.1 extracted from

  • Kim, J.; Mrksich, M.
    Profiling the selectivity of DNA ligases in an array format with mass spectrometry (2010), Nucleic Acids Res., 38, e2.
    View publication on PubMedView publication on EuropePMC

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Thermus aquaticus in the first, the ligase reacts with ATP to covalently modify an active site lysine residue with AMP. In the second step, the ligase transfers the AMP moiety to the 5' phosphate group of the substrate DNA strand. In the third step, the 3' hydroxyl group of the other strand reacts with the activated strand to give a native phosphodiester linkage with concomitant release of AMP ?
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?
additional information Tequatrovirus T4 in the first, the ligase reacts with ATP to covalently modify an active site lysine residue with AMP. In the second step, the ligase transfers the AMP moiety to the 5'-phosphate group of the substrate DNA strand. In the third step, the 3'-hydroxyl group of the other strand reacts with the activated strand to give a native phosphodiester linkage with concomitant release of AMP ?
-
?

Organism

Organism UniProt Comment Textmining
Tequatrovirus T4
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-
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Thermus aquaticus
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-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
adenosine 5'-[alpha-thio]-triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m the reaction rate is slower relative to reactions that use ATP. With adenosine 5'-[alpha-thio]-triphosphateas the cofactor, the ligase displays a significantly higher selectivity for ternary substrates having matched base pairs at the nick site Tequatrovirus T4 ?
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?
adenosine 5'-[alpha-thio]-triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m the reaction rate is slower relative to reactions that use ATP. With ATP-alphaS as the cofactor, the ligase displays a significantly higher selectivity for ternary substrates having matched base pairs at the nick site Thermus aquaticus ?
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?
adenosine 5'-[beta,gamma-imido]-triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m the ATP analogue has a different reactivity in the first reaction to adenylate the probe strand but the overall selectivity does not deviate from those observed when ATP is used Thermus aquaticus ?
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?
adenosine 5'-[beta,gamma-imido]-triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m the ATP analogue has a different reactivity in the first reaction to adenylate the probe strand but the overall selectivity does not deviate from those observed when ATP is used Tequatrovirus T4 ?
-
?
adenosine 5'-[gamma-thio]-triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m the ATP analogue has a different reactivity in the first reaction to adenylate the probe strand but the overall selectivity does not deviate from those observed when ATP is used Thermus aquaticus ?
-
?
adenosine 5'-[gamma-thio]-triphosphate + (deoxyribonucleotide)n + (deoxyribonucleotide)m the ATP analogue has a different reactivity in the first reaction to adenylate the probe strand but the overall selectivity does not deviate from those observed when ATP is used Tequatrovirus T4 ?
-
?
AMP + (deoxyribonucleotide)n + (deoxyribonucleotide)m the reaction rate is slower relative to reactions that use ATP Thermus aquaticus ?
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?
AMP + (deoxyribonucleotide)n + (deoxyribonucleotide)m the reaction rate is slower relative to reactions that use ATP Tequatrovirus T4 ?
-
?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
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Thermus aquaticus AMP + diphosphate + (deoxyribonucleotide)n+m
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?
ATP + (deoxyribonucleotide)n + (deoxyribonucleotide)m
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Tequatrovirus T4 AMP + diphosphate + (deoxyribonucleotide)n+m
-
?
additional information in the first, the ligase reacts with ATP to covalently modify an active site lysine residue with AMP. In the second step, the ligase transfers the AMP moiety to the 5' phosphate group of the substrate DNA strand. In the third step, the 3' hydroxyl group of the other strand reacts with the activated strand to give a native phosphodiester linkage with concomitant release of AMP Thermus aquaticus ?
-
?
additional information in the first, the ligase reacts with ATP to covalently modify an active site lysine residue with AMP. In the second step, the ligase transfers the AMP moiety to the 5'-phosphate group of the substrate DNA strand. In the third step, the 3'-hydroxyl group of the other strand reacts with the activated strand to give a native phosphodiester linkage with concomitant release of AMP Tequatrovirus T4 ?
-
?
additional information T4 ligase has a low specificity for adenylating the 5' strand, the ternary complexes having A:G, G:A and C:C mismatched base pairs are efficient substrates for adenylation even though they yield little ligated product Tequatrovirus T4 ?
-
?

Synonyms

Synonyms Comment Organism
ATP-dependent DNA ligase
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Thermus aquaticus
ATP-dependent DNA ligase
-
Tequatrovirus T4

Cofactor

Cofactor Comment Organism Structure
ATP
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Thermus aquaticus
ATP
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Tequatrovirus T4