Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA 2'-O-ribose C2498 methyltransferase

Gene: rlmM Accession Numbers: EG11794 (EcoCyc), b2806, ECK2801

Synonyms: ygdE, ribosomal RNA large subunit methyltransferase M

Regulation Summary Diagram: ?

Regulation summary diagram for rlmM

RlmM is the methyltransferase responsible for methylation of 23S rRNA at the 2'-O position of the ribose at the C2498 nucleotide within the peptidyl transferase loop. In vitro, the enzyme is active on naked 23S rRNA [Purta09, Punekar12] and unmodified domain V alone [Punekar12], but not assembled 50S ribosomal subunits or ribosomes [Purta09].

Crystal structures of RlmM have been solved [Punekar12, Guo13a], showing the presence of an N-terminal THUMP domain and aC-terminal Rossmann-like fold methyltransferase domain [Punekar12].

RlmM was predicted to be an RNA 2'-O-ribose methyltranserase by sequence similarity. The extended N-terminus may act in target recognition [Bujnicki00]. Phylogenetic analysis of this protein family has been performed [Feder03]. Phylogenetic profiling shows an unexplained link between RlmM and RdgC [Sergiev12].

An rlmM mutant has a slightly longer doubling time in rich medium than wild type and is slowly out-competed by wild type in a growth competition experiment [Purta09].

RlmM: "rRNA large subunit methyltransferase M" [Purta09]

Locations: cytosol

Map Position: [2,938,165 <- 2,939,265] (63.33 centisomes, 228°)
Length: 1101 bp / 366 aa

Molecular Weight of Polypeptide: 41.905 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0009197 , EchoBASE:EB1742 , EcoGene:EG11794 , EcoliWiki:b2806 , OU-Microarray:b2806 , PortEco:rlmM , PR:PRO_000023773 , Pride:P0ADR6 , Protein Model Portal:P0ADR6 , RefSeq:NP_417286 , RegulonDB:EG11794 , SMR:P0ADR6 , String:511145.b2806 , UniProt:P0ADR6

Relationship Links: InterPro:IN-FAMILY:IPR002877 , InterPro:IN-FAMILY:IPR011224 , InterPro:IN-FAMILY:IPR029063 , PDB:Structure:4ATN , PDB:Structure:4AUK , PDB:Structure:4B17 , Pfam:IN-FAMILY:PF01728

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0000453 - enzyme-directed rRNA 2'-O-methylation Inferred from experiment [Purta09]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a, GOA01a]
Molecular Function: GO:0070677 - rRNA (cytosine-2'-O-)-methyltransferase activity Inferred from experiment [Purta09]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008757 - S-adenosylmethionine-dependent methyltransferase activity Inferred by computational analysis [GOA06]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rlmM knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Last-Curated ? 10-Jun-2013 by Keseler I , SRI International

Enzymatic reaction of: 23S rRNA 2'-O-ribose C2498 methyltransferase

EC Number:

cytidine2498 in 23S rRNA + S-adenosyl-L-methionine <=> 2-O-methylcytidine2498 in 23S rRNA + S-adenosyl-L-homocysteine + H+

The reaction direction shown, that is, A + B ↔ C + D versus C + D ↔ A + B, is in accordance with the direction in which it was curated.

The reaction is physiologically favored in the direction shown.

Sequence Features

Protein sequence of 23S rRNA 2'-O-ribose C2498 methyltransferase with features indicated

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 188
[Punekar12, UniProt15]
UniProt: S-adenosyl-L-methionine.
Protein-Segment 221 -> 224
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest.
Amino-Acid-Sites-That-Bind 240
[Punekar12, UniProt15]
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 260
[Punekar12, UniProt15]
UniProt: S-adenosyl-L-methionine.
Amino-Acid-Sites-That-Bind 277
[Punekar12, UniProt15]
UniProt: S-adenosyl-L-methionine.
Active-Site 306
[Punekar12, UniProt15]
UniProt: Proton acceptor.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Peter D. Karp on Thu Jan 16, 2003:
Predicted gene function revised as a result of E. coli genome reannotation by Serres et al. [Serres01 ].
10/20/97 Gene b2806 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11794; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

Bujnicki00: Bujnicki JM, Rychlewski L (2000). "Prediction of a novel RNA 2'-O-ribose methyltransferase subfamily encoded by the Escherichia coli YgdE open reading frame and its orthologs." Acta Microbiol Pol 2000;49(3-4);253-60. PMID: 11293658

Feder03: Feder M, Pas J, Wyrwicz LS, Bujnicki JM (2003). "Molecular phylogenetics of the RrmJ/fibrillarin superfamily of ribose 2'-O-methyltransferases." Gene 302(1-2);129-38. PMID: 12527203

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Guo13a: Guo HY, Gao ZQ, Zhang H, Wei Y, Xu JH, Wang WY, Yan AX, Dong YH (2013). "Purification, crystallization and preliminary crystallographic analysis of the 23S rRNA methyltransferase RlmM (Cm2498) from Escherichia coli." Acta Crystallogr Sect F Struct Biol Cryst Commun 69(Pt 6);640-2. PMID: 23722841

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

Punekar12: Punekar AS, Shepherd TR, Liljeruhm J, Forster AC, Selmer M (2012). "Crystal structure of RlmM, the 2'O-ribose methyltransferase for C2498 of Escherichia coli 23S rRNA." Nucleic Acids Res 40(20);10507-20. PMID: 22923526

Purta09: Purta E, O'Connor M, Bujnicki JM, Douthwaite S (2009). "YgdE is the 2'-O-ribose methyltransferase RlmM specific for nucleotide C2498 in bacterial 23S rRNA." Mol Microbiol 72(5):1147-58. PMID: 19400805

Sergiev12: Sergiev PV, Golovina AY, Sergeeva OV, Osterman IA, Nesterchuk MV, Bogdanov AA, Dontsova OA (2012). "How much can we learn about the function of bacterial rRNA modification by mining large-scale experimental datasets?." Nucleic Acids Res 40(12);5694-705. PMID: 22411911

Serres01: Serres MH, Gopal S, Nahum LA, Liang P, Gaasterland T, Riley M (2001). "A functional update of the Escherichia coli K-12 genome." Genome Biol 2(9);RESEARCH0035. PMID: 11574054

UniProt12a: UniProt Consortium (2012). "UniProt version 2012-11 released on 2012-11-26 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11: UniProt-GOA (2011). "Gene Ontology annotation based on the manual assignment of UniProtKB Subcellular Location terms in UniProtKB/Swiss-Prot entries."

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
Page generated by SRI International Pathway Tools version 19.0 on Tue Oct 13, 2015, biocyc13.