BRENDA - Enzyme Database show
show all sequences of 2.1.1.264

Structure of the bifunctional methyltransferase YcbY (RlmKL) that adds the m7G2069 and m2G2445 modifications in Escherichia coli 23S rRNA

Wang, K.T.; Desmolaize, B.; Nan, J.; Zhang, X.W.; Li, L.F.; Douthwaite, S.; Su, X.D.; Nucleic Acids Res. 40, 5138-5148 (2012)

Data extracted from this reference:

Cloned(Commentary)
Commentary
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
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
Engineering
Amino acid exchange
Commentary
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
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
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
Primary Accession No. (UniProt)
Commentary
Textmining
Escherichia coli
-
gene rlmKL or ycbY
-
Escherichia coli BW25113
-
gene rlmKL or ycbY
-
Streptococcus mutans
-
-
-
Purification (Commentary)
Commentary
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
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
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
720601
Escherichia coli
?
-
-
-
-
additional information
Smu472 does not target G2445, and this nucleotide remains unmodified in Gram-positive rRNAs. Product identification by mass spectrometry
720601
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
720601
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
720601
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
720601
Escherichia coli BW25113
?
-
-
-
-
S-adenosyl-L-methionine + guanine2069 in 23S rRNA
-
720601
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
720601
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
720601
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
720601
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
720601
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
720601
Escherichia coli BW25113
S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
-
-
?
Subunits
Subunits
Commentary
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
Cofactor
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
-
Escherichia coli
S-adenosyl-L-methionine
-
Streptococcus mutans
Cloned(Commentary) (protein specific)
Commentary
Organism
gene ycbY, DNA and amino acid sequence determination and analysis, expression of His-tagged YcbY in Escherichiac coli strain BL21(DE3)
Escherichia coli
expression of His-tagged Smu472 in Escherichiac coli strain BL21(DE3)
Streptococcus mutans
Cofactor (protein specific)
Cofactor
Commentary
Organism
Structure
S-adenosyl-L-methionine
-
Escherichia coli
S-adenosyl-L-methionine
-
Streptococcus mutans
Crystallization (Commentary) (protein specific)
Crystallization
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
Engineering (protein specific)
Amino acid exchange
Commentary
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) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
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
-
-
?
Purification (Commentary) (protein specific)
Commentary
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) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
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
720601
Escherichia coli
?
-
-
-
-
additional information
Smu472 does not target G2445, and this nucleotide remains unmodified in Gram-positive rRNAs. Product identification by mass spectrometry
720601
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
720601
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
720601
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
720601
Escherichia coli BW25113
?
-
-
-
-
S-adenosyl-L-methionine + guanine2069 in 23S rRNA
-
720601
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
720601
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
720601
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
720601
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
720601
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
720601
Escherichia coli BW25113
S-adenosyl-L-homocysteine + N7-methylguanine2069 in 23S rRNA
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
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
General Information
General Information
Commentary
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
General Information (protein specific)
General Information
Commentary
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
Other publictions for EC 2.1.1.264
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
720987
Kita
Crystal structure of a putativ ...
Staphylococcus aureus
Protein Pept. Lett.
20
530-537
2013
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1
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3
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2
1
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1
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1
1
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2
1
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1
1
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-
720598
Kimura
Base methylations in the doubl ...
Escherichia coli, Neisseria meningitidis, Neisseria meningitidis MC58
Nucleic Acids Res.
40
4071-4085
2012
-
-
2
-
6
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-
-
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4
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3
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4
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1
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1
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1
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2
1
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6
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4
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4
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1
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1
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3
3
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720601
Wang
Structure of the bifunctional ...
Escherichia coli, Escherichia coli BW25113, Streptococcus mutans
Nucleic Acids Res.
40
5138-5148
2012
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2
2
1
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5
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32
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2
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11
2
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2
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2
2
2
1
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5
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2
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11
2
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3
3
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