Any feedback?
No. of entries
Information on EC 2.1.1.186 - 23S rRNA (cytidine2498-2'-O)-methyltransferase
for references in articles please use BRENDA:EC2.1.1.186
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree 2 Transferases
2.1 Transferring one-carbon groups
2.1.1 Methyltransferases
2.1.1.186 23S rRNA (cytidine2498-2'-O)-methyltransferase
The enzyme appears in viruses and cellular organisms
Reaction Schemes
show+
=
+
+
cytidine2498 in 23S rRNA
=
+
2'-O-methylcytidine2498 in 23S rRNA
Synonyms
rrna large subunit methyltransferase m, more
topPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
SYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
2O-ribose methyltransferase
RlmM
ygdE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA = S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
-
-
-
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
SYSTEMATIC NAME
IUBMB Comments
S-adenosyl-L-methionine:23S rRNA (cytidine2498-2?-O)-methyltransferase
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: YgdE is the 2'-O-methyltransferase responsible for modifying 23S rRNA nucleotide C2498. Modification occurs before assembly of the 50S ribosomal subunit
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: the recombinant YgdE methyltransferase modifies C2498 in naked 23S rRNA, but not in assembled 50S subunits or ribosomes. Nucleotide C2498 is situated within a highly conserved and heavily modified rRNA sequence, and the activity of YgdE is influenced by other modification enzymes that target this region
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: 23S rRNA substrate structure, overview. The S-adenosyl-L-methionine-binding site is open and shallow, suggesting that RNA substrate binding may be required to form a conformation needed for catalysis. RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: 23S rRNA substrate structure, overview. The S-adenosyl-L-methionine-binding site is open and shallow, suggesting that RNA substrate binding may be required to form a conformation needed for catalysis. RlmM uses one side of the two domains and the inter-domain linker to recognize its RNA substrate
Products: -
Products: -
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
LITERATURE
COMMENTARY
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: YgdE is the 2'-O-methyltransferase responsible for modifying 23S rRNA nucleotide C2498. Modification occurs before assembly of the 50S ribosomal subunit
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: -
Products: -
Products: -
?
S-adenosyl-L-methionine + cytidine2498 in 23S rRNA
S-adenosyl-L-homocysteine + 2'-O-methylcytidine2498 in 23S rRNA
Substrates: RlmM is active on 23S rRNA from an RlmM knockout strain but not on mature 50S subunits from the same strain
Products: -
Products: -
?
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
S-adenosyl-L-methionine
the S-adenosyl-L-methionine-binding site is open and shallow
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Highest Expressing Human Cell Lines
Cell Line LinksPlease wait a moment until the data is sorted. This message will disappear when the data is sorted.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
malfunction
C2498 methylation and the putative second methylation observed in the wild-type (YgdE+) strain are completely absent in the DygdE strain. Inactivation of the ygdE gene leads to loss of methylation at nucleotide C2498. The loss of ygdE function causes a slight reduction in bacterial fitness
physiological function
evolution
the catalytic domain of RlmM is closely related to YiiB, TlyA and fibrillarins, with the second K of the catalytic tetrad KDKE shifted by two residues at the C-terminal end of a beta strand compared with most 2'O MTases
evolution
-
the catalytic domain of RlmM is closely related to YiiB, TlyA and fibrillarins, with the second K of the catalytic tetrad KDKE shifted by two residues at the C-terminal end of a beta strand compared with most 2'O MTases
-
physiological function
RlmM catalyzes the S-adenosyl methionine-dependent 20O methylation of C2498 in 23S ribosomal RNA of Escherichia coli
physiological function
-
RlmM catalyzes the S-adenosyl methionine-dependent 20O methylation of C2498 in 23S ribosomal RNA of Escherichia coli
-
Show AA Sequence and Transmembrane Helices (2981 entries)
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please use the AA Sequence and Transmembrane Helices Search for a specific query.
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
PDB
SCOP
CATH
UNIPROT
ORGANISM
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
RlmM consists of an N-terminal THUMP domain and a C-terminal catalytic Rossmann-like fold MTase domain in a distinct arrangement, detailed structure analysis, overview
additional information
-
RlmM consists of an N-terminal THUMP domain and a C-terminal catalytic Rossmann-like fold MTase domain in a distinct arrangement, detailed structure analysis, overview
-
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
in complex with S-adenosyl-L-methionine, sitting drop vapor diffusion method, using 16% (w/v) polyethylene glycol 3350, 0.05 M citric acid, 0.05 M bis-tris propane pH 5.0
purified recombinant His-tagged RlmM free or in complex with S-adenosyl-L-methionine, sitting drop vapor diffusion method, 0.0015 ml 10 mg/ml protein solution os mixed with 0.0015 ml of reservoir solution containing 0.3 M ammonium tartrate, pH 7.0, and 20% PEG 3350, 20°C, 1 week, two crystal forms, X-ray diffraction structure determination and analysis at 1.9 A and 2.6 A resolution, respectively, molecular replacement
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
Na2SO4 gives the highest thermal stability to RlmM
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
nickel-nitrilotriacetic acid resin column chromatography, heparin column chromatography, and Superdex 75 gel filtration
recombinant His-tagged RlmM from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, gel filtration, and ultrafiltration
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene rlmM, expression of His-tagged RlmM in Escherichia coli strain BL21(DE3)
Please wait a moment until the data is sorted. This message will disappear when the data is sorted.
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Purta, E.; O'Connor, M.; Bujnicki, J.M.; Douthwaite, S.
YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA
Mol. Microbiol.
72
1147-1158
2009
Escherichia coli (P0ADR6), Escherichia coli
brenda
Punekar, A.S.; Shepherd, T.R.; Liljeruhm, J.; Forster, A.C.; Selmer, M.
Crystal structure of RlmM, the 2O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA
Nucleic Acids Res.
40
10507-10520
2012
Escherichia coli (P0ADR6), Escherichia coli BW25113 (P0ADR6)
brenda
Guo, H.Y.; Gao, Z.Q.; Zhang, H.; Wei, Y.; Xu, J.H.; Wang, W.Y.; Yan, A.X.; Dong, Y.H.
Purification, crystallization and preliminary crystallographic analysis of the 23S rRNA methyltransferase RlmM (Cm2498) from Escherichia coli
Acta Crystallogr. Sect. F
69
640-642
2013
Escherichia coli (P0ADR6)
brenda
EXTERNAL LINKS (specific for EC-Number 2.1.1.186)
html completed
Use of this online version of BRENDA is free under the CC BY 4.0 license. See terms of use for full details.
Release 2026.1 (March 2026)
About BRENDA
Social media
Help
Survey
Download
Contribution
Legal
Curated at
Member of
![DSMZ Digital Diversity]()
![Global Core Biodata Resource]()
![ELIXIR Core Data Resource]()
![German Network for Bioinformatics Infrastructure]()
