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Literature summary 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

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.1.1.264 expression of His-tagged Smu472 in Escherichiac coli strain BL21(DE3) Streptococcus mutans
2.1.1.264 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)

EC Number Crystallization (Comment) Organism
2.1.1.264 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
2.1.1.264 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

EC Number Protein Variants Comment Organism
2.1.1.173 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
2.1.1.264 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)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.1.1.173 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 ?
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2069 in 23S rRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2445 in 23S rRNA Escherichia coli
-
 S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2445 in 23S rRNA Streptococcus mutans Smu472 adds the m2G2445 modification S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
-
 ?
2.1.1.264 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 ?
-
 ?
2.1.1.264 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 ?
-
 ?
2.1.1.264 S-adenosyl-L-methionine + guanine2069 in 23S rRNA Streptococcus mutans
-
 S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
2.1.1.264 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
-
 ?
2.1.1.264 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

EC Number Organism UniProt Comment Textmining
2.1.1.173 Escherichia coli P75864 gene ycbY
-
2.1.1.173 Streptococcus mutans
-
-
-
2.1.1.264 Escherichia coli
-
 gene rlmKL or ycbY
-
2.1.1.264 Escherichia coli BW25113
-
 gene rlmKL or ycbY
-
2.1.1.264 Streptococcus mutans
-
-
-

Purification (Commentary)

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

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.1.1.173 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 ?
-
 ?
2.1.1.173 additional information Smu776 does not target G2069, and this nucleotide remains unmodified in Gram-positive rRNAs Streptococcus mutans ?
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2069 in 23S rRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2069 in 23S rRNA m7G2069 modification by YcbY is stoichiometric Escherichia coli S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2445 in 23S rRNA
-
 Streptococcus mutans S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2445 in 23S rRNA
-
 Escherichia coli S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2445 in 23S rRNA Smu472 adds the m2G2445 modification Streptococcus mutans S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
-
 ?
2.1.1.173 S-adenosyl-L-methionine + guanine2445 in 23S rRNA m2G2445 modification by YcbY is stoichiometric Escherichia coli S-adenosyl-L-homocysteine + N2-methylguanine2445 in 23S rRNA
-
 ?
2.1.1.264 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 ?
-
 ?
2.1.1.264 additional information Smu472 does not target G2445, and this nucleotide remains unmodified in Gram-positive rRNAs. Product identification by mass spectrometry Streptococcus mutans ?
-
 ?
2.1.1.264 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 ?
-
 ?
2.1.1.264 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 ?
-
 ?
2.1.1.264 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 ?
-
 ?
2.1.1.264 S-adenosyl-L-methionine + guanine2069 in 23S rRNA
-
 Streptococcus mutans S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
 ?
2.1.1.264 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
-
 ?
2.1.1.264 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
-
 ?
2.1.1.264 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
-
 ?
2.1.1.264 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
-
 ?
2.1.1.264 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

EC Number Subunits Comment Organism
2.1.1.173 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
2.1.1.173 More structure comparisosns with Streptococcus mutans proteins Smu472 and Smu776, the active site and their folding patterns respectively resemble each other, overview Escherichia coli
2.1.1.264 More structure comparisons with Streptococcus mutans proteins Smu472 and Smu776, the active site and their folding patterns respectively resemble each other, overview Escherichia coli
2.1.1.264 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

EC Number Synonyms Comment Organism
2.1.1.173 m2G2445 methyltransferase
-
 Streptococcus mutans
2.1.1.173 m2G2445 methyltransferase
-
 Escherichia coli
2.1.1.173 ribosomal large subunit methyltransferase
-
 Escherichia coli
2.1.1.173 RlmKL
-
 Escherichia coli
2.1.1.173 Smu472
-
 Streptococcus mutans
2.1.1.173 ycbY
-
 Escherichia coli
2.1.1.264 bifunctional methyltransferase
-
 Escherichia coli
2.1.1.264 m2G2069 methyltransferase
-
 Streptococcus mutans
2.1.1.264 ribosomal large subunit methyltransferase
-
 Escherichia coli
2.1.1.264 RlmKL
-
 Escherichia coli
2.1.1.264 Smu472
-
 Streptococcus mutans
2.1.1.264 ycbY
-
 Escherichia coli

Cofactor

EC Number Cofactor Comment Organism Structure
2.1.1.173 S-adenosyl-L-methionine
-
 Streptococcus mutans
2.1.1.173 S-adenosyl-L-methionine
-
 Escherichia coli
2.1.1.264 S-adenosyl-L-methionine
-
 Escherichia coli
2.1.1.264 S-adenosyl-L-methionine
-
 Streptococcus mutans

General Information

EC Number General Information Comment Organism
2.1.1.173 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
2.1.1.173 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 Escherichia coli
2.1.1.173 physiological function 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
2.1.1.264 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
2.1.1.264 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
2.1.1.264 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