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Information on EC 2.1.1.171 - 16S rRNA (guanine966-N2)-methyltransferase and Organism(s) Escherichia coli and UniProt Accession P0ADX9

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EC Tree
IUBMB Comments
The enzyme efficiently methylates guanine966 of the assembled 30S subunits in vitro. Protein-free 16S rRNA is not a substrate for RsmD . The enzyme specifically methylates guanine966 at N2 in 16S rRNA.
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This record set is specific for:
Escherichia coli
UNIPROT: P0ADX9
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The taxonomic range for the selected organisms is: Escherichia coli
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Reaction Schemes
hide
S-adenosyl-L-methionine
+
guanine966 in 16S rRNA
=
S-adenosyl-L-homocysteine
+
N2-methylguanine966 in 16S rRNA
+
guanine966 in 16S rRNA
=
+
N2-methylguanine966 in 16S rRNA
Synonyms
rv2966c, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
16S rRNA-specific methyltransferases m2GMT
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m2G966 methyltransferase
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RNA:(guanine-N2) methyltransferase RsmD
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small rRNA methyltransferase
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-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + guanine966 in 16S rRNA = S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA
show the reaction diagram
proposed model of rRNA/RsmD interactions in the active site
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:16S rRNA (guanine966-N2)-methyltransferase
The enzyme efficiently methylates guanine966 of the assembled 30S subunits in vitro. Protein-free 16S rRNA is not a substrate for RsmD [1]. The enzyme specifically methylates guanine966 at N2 in 16S rRNA.
CAS REGISTRY NUMBER
COMMENTARY hide
50812-26-5
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine966 in 16S rRNA
S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA
show the reaction diagram
S-adenosyl-L-methionine + guanine966 in 16S rRNA
S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA
show the reaction diagram
S-adenosyl-L-methionine + guanine966 in 30S rRNA
S-adenosyl-L-homocysteine + N2-methylguanine966 in 30S rRNA
show the reaction diagram
additional information
?
-
-
RsmD possesses superior binding properties toward the unmodified 30S subunit but is unable to bind a 30S subunit modified at G966
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + guanine966 in 16S rRNA
S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA
show the reaction diagram
S-adenosyl-L-methionine + guanine966 in 16S rRNA
S-adenosyl-L-homocysteine + N2-methylguanine966 in 16S rRNA
show the reaction diagram
-
-
-
-
?
S-adenosyl-L-methionine + guanine966 in 30S rRNA
S-adenosyl-L-homocysteine + N2-methylguanine966 in 30S rRNA
show the reaction diagram
-
RsmD acts late in the assembly process and is able to modify a completely assembled 30S subunit
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
S-adenosyl-L-methionine
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S-adenosyl-L-methionine
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-
additional information
-
sinefungin is an unreactive S-adenosyl-L-methionine analogue
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
additional information
-
RsmD methyltransferase kinetics, multiple turnover reaction, overview
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
disruption of the yhhF gene by kanamycin resistance marker leads to a loss of modification at guanine966. Doubling of strain JW3430 carrying the inactive rsmD gene is essentially the same as that of the parental Escherichia coli strain BW25141
malfunction
additional information
-
RsmD is unusual in its ability to withstand multiple amino acid substitutions of the active site. Such efficiency of RsmD may be useful to complete the modification of a 30S subunit ahead of the 30S subunit's involvement in translation
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
based on a comprehensive bioinformatic analysis of m2G methyltransferases it is inferred that the prokaryotic RsmC and RsmD methyltransferases are pseudodimers. The C-terminal catalytic domain is closely related to the structurally characterized Mj0882 protein, while the N-terminal domain lacks the cofactor-binding and catalytic side-chains
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
vapor diffusion method in hanging drops, structure determined and refined to 2.05 A
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D58A
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site-directed mutagenesis, the mutant shows increased Km toward the 30S subunit by two orders of magnitude with only a marginal effect on kcat compared to the wild-type enzyme. The mutation decreases the enthalpic contribution to SAM binding, paralleled by an increase in the entropic contribution
D58A/P128A/P129A
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site-directed mutagenesis, the mutant shows increased Km toward the 30S subunit by two orders of magnitude with only a marginal effect on kcat compared to the wild-type enzyme
F130S
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site-directed mutagenesis
P128A/P129A
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site-directed mutagenesis, the mutation decreases the enthalpic contribution to SAM binding, paralleled by an increase in the entropic contribution,
P128A/P129A/F130S
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site-directed mutagenesis, inactive mutant
additional information
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knockout of the rsmD gene and complementation by point mutants, except for mutant P128A/P129A/F130S, overview
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene rsmD, expression of N-terminally His6-tagged RsmD
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REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Lesnyak, D.V.; Osipiuk, J.; Skarina, T.; Sergiev, P.V.; Bogdanov, A.A.; Edwards, A.; Savchenko, A.; Joachimiak, A.; Dontsova, O.A.
Methyltransferase that modifies guanine 966 of the 16 S rRNA: functional identification and tertiary structure
J. Biol. Chem.
282
5880-5887
2007
Escherichia coli (P0ADX9)
Manually annotated by BRENDA team
Sergiev, P.V.; Bogdanov, A.A.; Dontsova, O.A.
Ribosomal RNA guanine-(N2)-methyltransferases and their targets
Nucleic Acids Res.
35
2295-2301
2007
Escherichia coli (P0ADX9)
Manually annotated by BRENDA team
Bujnicki, J.M.
Rychlewski. L.: RNA:(guanine-N2) methyltransferases RsmC/RsmD and their homologs revisited--bioinformatic analysis and prediction of the active site based on the uncharacterized Mj0882 protein structure
BMC Bioinformatics
3
10
2002
Escherichia coli (P0ADX9)
Manually annotated by BRENDA team
Weitzmann, C.; Tumminia, S.J.; Boublik, M.; Ofengand, J.
A paradigm for local conformational control of function in the ribosome: binding of ribosomal protein S19 to Escherichia coli 16S rRNA in the presence of 57 is required for methylation of m2G966 and blocks methylation of m C967 by their respective methyltransferases
Nucleic Acids Res.
19
7089-7095
1991
Escherichia coli (P0ADX9)
Manually annotated by BRENDA team
Sergeeva, O.V.; Prokhorova, I.V.; Ordabaev, Y.; Tsvetkov, P.O.; Sergiev, P.V.; Bogdanov, A.A.; Makarov, A.A.; Dontsova, O.A.
Properties of small rRNA methyltransferase RsmD: mutational and kinetic study
RNA
18
1178-1185
2012
Escherichia coli
Manually annotated by BRENDA team
Arora, S.; Bhamidimarri, S.P.; Weber, M.H.; Varshney, U.
Role of the ribosomal P-site elements of m2G966, m5C967, and the S9 C-terminal tail in maintenance of the reading frame during translational elongation in Escherichia coli
J. Bacteriol.
195
3524-3530
2013
Escherichia coli, Escherichia coli BW25113
Manually annotated by BRENDA team
Arora, S.; Bhamidimarri, S.P.; Bhattacharyya, M.; Govindan, A.; Weber, M.H.; Vishveshwara, S.; Varshney, U.
Distinctive contributions of the ribosomal P-site elements m2G966, m5C967 and the C-terminal tail of the S9 protein in the fidelity of initiation of translation in Escherichia coli
Nucleic Acids Res.
41
4963-4975
2013
Escherichia coli
Manually annotated by BRENDA team