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Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA 2'-O-ribose G2251 methyltransferase



Gene: rlmB Accession Numbers: G7845 (EcoCyc), b4180, ECK4176

Synonyms: yjfH

Regulation Summary Diagram: ?

Subunit composition of 23S rRNA 2'-O-ribose G2251 methyltransferase = [RlmB]2
         23S rRNA 2'-O-ribose G2251 methyltransferase monomer = RlmB

Summary:
RlmB is the methyltransferase responsible for methylation of 23S rRNA at the 2'-O position of the ribose at the G2251 nucleotide [Lovgren01].

RlmB is a 2'O-methyltransferase that belongs to the SPOUT superfamily [Michel02]. A crystal structure of RlmB has been solved at 2.5 Å resolution. The N terminus is implicated in rRNA recognition, and the C-terminal domain contains a deep knot structure that encompasses the predicted SAM binding site [Michel02]. Computational docking analysis of the SAM binding site allowed inference of functionally important residues and a reaction mechanism [Kurowski03].

An rlmB deletion mutant does not show growth defects or defects in ribosome maturation [Lovgren01].

RlmB: "rRNA large subunit methyltransferase B" [Lovgren01]

Gene Citations: [Cairrao03]

Locations: cytosol

Map Position: [4,407,298 -> 4,408,029] (94.99 centisomes)
Length: 732 bp / 243 aa

Molecular Weight of Polypeptide: 26.557 kD (from nucleotide sequence)

Molecular Weight of Multimer: 60.0 kD (experimental) [Michel02]

Unification Links: ASAP:ABE-0013684 , DIP:DIP-47866N , EchoBASE:EB2376 , EcoGene:EG12483 , EcoliWiki:b4180 , ModBase:P63177 , OU-Microarray:b4180 , PortEco:rlmB , PR:PRO_000023766 , Pride:P63177 , Protein Model Portal:P63177 , RefSeq:NP_418601 , RegulonDB:G7845 , SMR:P63177 , String:511145.b4180 , UniProt:P63177

Relationship Links: InterPro:IN-FAMILY:IPR001537 , InterPro:IN-FAMILY:IPR004441 , InterPro:IN-FAMILY:IPR013123 , InterPro:IN-FAMILY:IPR024915 , PDB:Structure:1GZ0 , Pfam:IN-FAMILY:PF00588 , Pfam:IN-FAMILY:PF08032 , Smart:IN-FAMILY:SM00967

In Paralogous Gene Group: 435 (4 members)

Gene-Reaction Schematic: ?

GO Terms:

Biological Process: GO:0000453 - enzyme-directed rRNA 2'-O-methylation Inferred from experiment [Lovgren01]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a, GOA06]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0070039 - rRNA (guanosine-2'-O-)-methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Lovgren01]
GO:0003723 - RNA binding Inferred by computational analysis [GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008173 - RNA methyltransferase activity Inferred by computational analysis [GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
Cellular Component: GO:0005829 - cytosol Inferred from experiment Inferred by computational analysis [DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rlmB 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]

Credits:
Last-Curated ? 17-Sep-2008 by Keseler I , SRI International


Enzymatic reaction of: 23S rRNA 2'-O-ribose G2251 methyltransferase

EC Number: 2.1.1.185

guanosine2251 in 23S rRNA + S-adenosyl-L-methionine <=> 2-O-methylguanosine2251 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 of enzyme catalysis.

The reaction is physiologically favored in the direction shown.


Sequence Features

Feature Class Location Citations Comment
Amino-Acid-Sites-That-Bind 196
[UniProt10]
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 216
[UniProt10]
UniProt: S-adenosyl-L-methionine; via amide nitrogen and carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 225
[UniProt10]
UniProt: S-adenosyl-L-methionine; via amide nitrogen; Non-Experimental Qualifier: by similarity;


Gene Local Context (not to scale): ?

Transcription Units:

Notes:

History:
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


References

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

Cairrao03: Cairrao F, Cruz A, Mori H, Arraiano CM (2003). "Cold shock induction of RNase R and its role in the maturation of the quality control mediator SsrA/tmRNA." Mol Microbiol 50(4);1349-60. PMID: 14622421

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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."

Ishihama08: Ishihama Y, Schmidt T, Rappsilber J, Mann M, Hartl FU, Kerner MJ, Frishman D (2008). "Protein abundance profiling of the Escherichia coli cytosol." BMC Genomics 9;102. PMID: 18304323

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

Kurowski03: Kurowski MA, Sasin JM, Feder M, Debski J, Bujnicki JM (2003). "Characterization of the cofactor-binding site in the SPOUT-fold methyltransferases by computational docking of S-adenosylmethionine to three crystal structures." BMC Bioinformatics 4;9. PMID: 12689347

LopezCampistrou05: Lopez-Campistrous A, Semchuk P, Burke L, Palmer-Stone T, Brokx SJ, Broderick G, Bottorff D, Bolch S, Weiner JH, Ellison MJ (2005). "Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth." Mol Cell Proteomics 4(8);1205-9. PMID: 15911532

Lovgren01: Lovgren JM, Wikstrom PM (2001). "The rlmB gene is essential for formation of Gm2251 in 23S rRNA but not for ribosome maturation in Escherichia coli." J Bacteriol 183(23);6957-60. PMID: 11698387

Michel02: Michel G, Sauve V, Larocque R, Li Y, Matte A, Cygler M (2002). "The structure of the RlmB 23S rRNA methyltransferase reveals a new methyltransferase fold with a unique knot." Structure (Camb) 10(10);1303-15. PMID: 12377117

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 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."


Report Errors or Provide Feedback
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 18.5 on Sun Nov 23, 2014, BIOCYC13A.