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Literature summary for 2.1.1.264 extracted from

  • Wang, K.T.; Desmolaize, B.; Nan, J.; Zhang, X.W.; Li, L.F.; Douthwaite, S.; Su, X.D.
    Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA (2012), Nucleic Acids Res., 40, 5138-5148.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 2.1.1.264

Cloned(Commentary)

Cloned (Comment) Organism
expression of His-tagged Smu472 in Escherichiac coli strain BL21(DE3) Streptococcus mutans
gene ycbY, DNA and amino acid sequence determination and analysis, expression of His-tagged YcbY in Escherichiac coli strain BL21(DE3) Escherichia coli

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant Smu472, in presence of S-adenosyl-L-methionine and S-adenosyl-L-homocysteine, hanging drop or sitting drop vapor diffusion method, 16°C, X-ray diffraction structure determination and analysis Streptococcus mutans
purified recombinant YcbY, in presence of S-adenosyl-L-methionine and S-adenosyl-L-homocysteine, hanging drop or sitting drop vapor diffusion method, 16°C, X-ray diffraction structure determination and analysis Escherichia coli

Protein Variants

Protein Variants Comment Organism
additional information generation of a ycbY knock-out strain, completely inactive in methylation, from Escherichia coli strain BW25113 and complementation with active ycbY Escherichia coli

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
additional information Escherichia coli the bifunctional methyltransferase YcbY, i.e. RlmKL, adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA, recognition of dual rRNA targets by YcbY ?
-
 ?
additional information Escherichia coli BW25113 the bifunctional methyltransferase YcbY, i.e. RlmKL, adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA, recognition of dual rRNA targets by YcbY ?
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA Streptococcus mutans
-
 S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA Escherichia coli RlmK activity in helix 74 of Escherichia coli 23S rRNA S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA Escherichia coli BW25113 RlmK activity in helix 74 of Escherichia coli 23S rRNA S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?

Organism

Organism UniProt Comment Textmining
Escherichia coli
-
 gene rlmKL or ycbY
-
Escherichia coli BW25113
-
 gene rlmKL or ycbY
-
Streptococcus mutans
-
-
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged Smu472 from Escherichiac coli strain BL21(DE3) by nickel affinity chromatography Streptococcus mutans
recombinant His-tagged YcbY from Escherichiac coli strain BL21(DE3) by nickel affinity chromatography Escherichia coli

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information the bifunctional methyltransferase YcbY, i.e. RlmKL, adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA, recognition of dual rRNA targets by YcbY Escherichia coli ?
-
 ?
additional information Smu472 does not target G2445, and this nucleotide remains unmodified in Gram-positive rRNAs. Product identification by mass spectrometry Streptococcus mutans ?
-
 ?
additional information the enzyme also catalyzes the N2-methylation of guanine2445 in 23S rRNA, RlmL activity, reaction of EC 2.1.1.173. Product identification by mass spectrometry Escherichia coli ?
-
 ?
additional information the bifunctional methyltransferase YcbY, i.e. RlmKL, adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA, recognition of dual rRNA targets by YcbY Escherichia coli BW25113 ?
-
 ?
additional information the enzyme also catalyzes the N2-methylation of guanine2445 in 23S rRNA, RlmL activity, reaction of EC 2.1.1.173. Product identification by mass spectrometry Escherichia coli BW25113 ?
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA
-
 Streptococcus mutans S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA RlmK activity in helix 74 of Escherichia coli 23S rRNA Escherichia coli S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA methylation sites in the peptidyl transferase region of Escherichia coli 23S rRNA. structure, overview Streptococcus mutans S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA RlmK activity in helix 74 of Escherichia coli 23S rRNA, methylation sites in the peptidyl transferase region of Escherichia coli 23S rRNA. structure, overview Escherichia coli S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA RlmK activity in helix 74 of Escherichia coli 23S rRNA Escherichia coli BW25113 S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
S-adenosyl-L-methionine + guanine2069 in 23S rRNA RlmK activity in helix 74 of Escherichia coli 23S rRNA, methylation sites in the peptidyl transferase region of Escherichia coli 23S rRNA. structure, overview Escherichia coli BW25113 S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?

Subunits

Subunits Comment Organism
More structure comparisons with Streptococcus mutans proteins Smu472 and Smu776, the active site and their folding patterns respectively resemble each other, overview Escherichia coli
More structure comparisosns of Streptococcus mutans proteins Smu472 and Smu776 with Escherichia coli RlmKL protein, the active site and their folding patterns respectively resemble each other, overview Streptococcus mutans

Synonyms

Synonyms Comment Organism
bifunctional methyltransferase
-
 Escherichia coli
m2G2069 methyltransferase
-
 Streptococcus mutans
ribosomal large subunit methyltransferase
-
 Escherichia coli
RlmKL
-
 Escherichia coli
Smu472
-
 Streptococcus mutans
ycbY
-
 Escherichia coli

Cofactor

Cofactor Comment Organism Structure
S-adenosyl-L-methionine
-
 Escherichia coli
S-adenosyl-L-methionine
-
 Streptococcus mutans

General Information

General Information Comment Organism
evolution the enzyme is a member of the COG1092 family, evolutionary implications of the apparent emergence of Escherichia coli YcbY from the fusion of Streptococcus mutans Smu472 and Smu776 orthologues are considered, Streptococcus mutans proteins Smu472 and Smu776 are respectively Gram-positive orthologs of the N- and C-halves of YcbY Escherichia coli
evolution the enzyme is a member of the COG1092 family, evolutionary implications of the apparent emergence of Escherichia coli YcbY from the fusion of Streptococcus mutans Smu472 and Smu776 orthologues are considered, Streptococcus mutans proteins Smu472 and Smu776 are respectively Gram-positive orthologs of the N- and C-halves of YcbY Streptococcus mutans
physiological function the YcbY enzyme is a methyltransferase catalyzing two mechanistically different types of RNA modification. The N-terminal region of YcbY adds the m2G2445 modification, while the C-terminal region of YcbY is responsible for the m7G2069 methylation on the opposite side of the same helix, H74. YcbY enzyme is an example of a methyltransferase catalyzing two mechanistically different types of RNA modification Escherichia coli