Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA m5C1962 methyltransferase

Gene: rlmI Accession Numbers: G6501 (EcoCyc), b0967, ECK0958

Synonyms: yccW, ribosomal RNA large subunit methyltransferase I

Regulation Summary Diagram: ?

Regulation summary diagram for rlmI

Subunit composition of 23S rRNA m5C1962 methyltransferase = [RlmI]2
         23S rRNA m5C1962 methyltransferase monomer = RlmI

RlmI is the methyltransferase responsible for methylation of 23S rRNA at the C5 position of the C1962 nucleotide. The enzyme can methylate naked 23S rRNA, but not assembled 50S ribosomal subunits or 70S ribosomes [Purta08].

A crystal structure of RlmI has been solved at 2 Å resolution; domain organization and possible evolutionary relationships of the enzyme are discussed [Sunita08].

A mutant with a deletion of rlmI shows a significant decrease in biofilm formation [Herzberg06]. However, an rlmI mutant shows only a slight growth defect compared to wild-type cells during competitive growth experiments in rich or minimal medium [Purta08].

Expression of rlmI increases 17-fold upon deletion of tqsA, which increases biofilm formation [Herzberg06].

RlmI: "rRNA large subunit methyltransferase I" [Purta08]

Review: [Motorin10]

Locations: cytosol

Map Position: [1,028,002 <- 1,029,192] (22.16 centisomes, 80°)
Length: 1191 bp / 396 aa

Molecular Weight of Polypeptide: 44.357 kD (from nucleotide sequence)

Molecular Weight of Multimer: 100.0 kD (experimental) [Sunita08]

Unification Links: ASAP:ABE-0003272 , DIP:DIP-11501N , EchoBASE:EB3489 , EcoGene:EG13725 , EcoliWiki:b0967 , ModBase:P75876 , OU-Microarray:b0967 , PortEco:rlmI , PR:PRO_000023771 , Protein Model Portal:P75876 , RefSeq:NP_415487 , RegulonDB:G6501 , SMR:P75876 , String:511145.b0967 , UniProt:P75876

Relationship Links: InterPro:IN-FAMILY:IPR002478 , InterPro:IN-FAMILY:IPR015947 , InterPro:IN-FAMILY:IPR019614 , InterPro:IN-FAMILY:IPR023542 , InterPro:IN-FAMILY:IPR029063 , PDB:Structure:3C0K , Pfam:IN-FAMILY:PF10672 , Prosite:IN-FAMILY:PS50890 , Smart:IN-FAMILY:SM00359

In Paralogous Gene Group: 229 (2 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0031167 - rRNA methylation Inferred from experiment Inferred by computational analysis [GOA06, Purta08]
GO:0042710 - biofilm formation Inferred from experiment [Herzberg06]
GO:0070475 - rRNA base methylation Inferred from experiment [Purta08]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0009383 - rRNA (cytosine-C5-)-methyltransferase activity Inferred from experiment [Purta08]
GO:0016434 - rRNA (cytosine) methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, Purta08]
GO:0003723 - RNA binding Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0008649 - rRNA 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]
GO:0005737 - cytoplasm Inferred by curator Inferred by computational analysis [UniProtGOA11, UniProtGOA11a, GOA06, Purta08]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rlmI 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]

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

Enzymatic reaction of: 23S rRNA m5C1962 methyltransferase

EC Number:

cytosine1962 in 23S rRNA + S-adenosyl-L-methionine <=> 5-methylcytosine1962 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 m5C1962 methyltransferase monomer with features indicated

Feature Class Location Citations Comment
Conserved-Region 2 -> 81
UniProt: PUA;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


Ingrid Keseler on Tue Sep 16, 2008:
Gene start position changed based on [Purta08 ].
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 ].
Markus Krummenacker on Tue Oct 14, 1997:
Gene object created from Blattner lab Genbank (v. M52) entry.


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

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."

Herzberg06: Herzberg M, Kaye IK, Peti W, Wood TK (2006). "YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport." J Bacteriol 188(2);587-98. PMID: 16385049

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

Motorin10: Motorin Y, Lyko F, Helm M (2010). "5-methylcytosine in RNA: detection, enzymatic formation and biological functions." Nucleic Acids Res 38(5);1415-30. PMID: 20007150

Purta08: Purta E, O'Connor M, Bujnicki JM, Douthwaite S (2008). "YccW is the m(5)C methyltransferase specific for 23S rRNA nucleotide 1962." J Mol Biol 383(3):641-51. PMID: 18786544

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

Sunita08: Sunita S, Tkaczuk KL, Purta E, Kasprzak JM, Douthwaite S, Bujnicki JM, Sivaraman J (2008). "Crystal Structure of the Escherichia coli 23S rRNA:m(5)C Methyltransferase RlmI (YccW) Reveals Evolutionary Links between RNA Modification Enzymes." J Mol Biol 383(3):652-66. PMID: 18789337

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 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
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