Escherichia coli K-12 substr. MG1655 Enzyme: 23S rRNA m1G745 methyltransferase

Gene: rlmA Accession Numbers: EG12207 (EcoCyc), b1822, ECK1820

Synonyms: rrmA, yebH, ribosomal RNA large subunit methyltransferase A, rRNA large subunit methyltransferase A

Regulation Summary Diagram: ?

Regulation summary diagram for rlmA

RlmA is the methyltransferase responsible for methylation of 23S rRNA at the N1 position of the G745 nucleotide. RlmA activity is required for wild-type translation and cell growth [Gustafsson98]. The methylated base is expected to reside near the peptide exit channel in the context of the ribosome [Hansen01a].

In vitro, RlmA is able to methylate free 23S rRNA, but not assembled 50S ribosomal subunits or 70S ribosomes. A 92 nt fragment of 23S rRNA consisting of stem-loops 33, 34 and 35 is efficiently methylated [Hansen01a]. Specificity for the target nucleotide is determined by the methyltransferase rather than the rRNA substrate [Liu02].

The location of the SAM-binding region and catalytic site have been predicted . RlmA is predicted to have an N-terminal zinc finger and a C-terminal substrate recognition region [Bujnicki02a]. The crystal structure of RlmA has been determined at 2.8 Å resolution, and RlmA appears to be an asymmetric dimer. The Zn2+-binding domains may be responsible for RNA recognition and binding [Das04].

An rlmA mutant lacks 1-methylguanine in its rRNA [Isaksson73]. rlmA mutants exhibit defects in translation, a decreased growth rate even in rich medium, and increased resistance to the antibiotic viomycin [Gustafsson98]. However, the growth defect of an rlmA mutant is not due to lack of rRNA methylation, and thus RlmA appears to have another, as yet unidentified, function [Liu04c].

RlmAI: "rRNA large subunit methyltransferase A" [Liu02]

Locations: cytosol

Map Position: [1,904,275 <- 1,905,084] (41.04 centisomes, 148°)
Length: 810 bp / 269 aa

Molecular Weight of Polypeptide: 30.419 kD (from nucleotide sequence)

Unification Links: ASAP:ABE-0006067 , EchoBASE:EB2122 , EcoGene:EG12207 , EcoliWiki:b1822 , ModBase:P36999 , OU-Microarray:b1822 , PortEco:rrmA , PR:PRO_000023765 , Protein Model Portal:P36999 , RefSeq:NP_416336 , RegulonDB:EG12207 , SMR:P36999 , String:511145.b1822 , UniProt:P36999

Relationship Links: InterPro:IN-FAMILY:IPR016718 , InterPro:IN-FAMILY:IPR025714 , InterPro:IN-FAMILY:IPR029063 , PDB:Structure:1P91 , Pfam:IN-FAMILY:PF13847

In Paralogous Gene Group: 194 (13 members)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

GO Terms:

Biological Process: GO:0070475 - rRNA base methylation Inferred from experiment [Gustafsson98]
GO:0006364 - rRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0008270 - zinc ion binding Inferred from experiment [Das04]
GO:0008989 - rRNA (guanine-N1-)-methyltransferase activity Inferred from experiment [Hansen01a]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a, GOA01a]
GO:0016740 - transferase activity Inferred by computational analysis [UniProtGOA11a]
GO:0046872 - metal ion binding Inferred by computational analysis [UniProtGOA11a]
GO:0052911 - 23S rRNA (guanine(745)-N(1))-methyltransferase activity Inferred by computational analysis [GOA01]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for rlmA knockouts: ?

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

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

Enzymatic reaction of: 23S rRNA m1G745 methyltransferase

Synonyms: rRNA (guanine-N1-)-methyltransferase, S-adenosyl-L-methionine:rRNA (guanine-N1-)-methyltransferase, ribosomal ribonucleate guanine 1-methyltransferase

EC Number:

guanine745 in 23S rRNA + S-adenosyl-L-methionine <=> N1-methylguanine745 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.

Cofactors or Prosthetic Groups: Zn2+ [Das04]

Sequence Features

Protein sequence of 23S rRNA m1G745 methyltransferase with features indicated

Feature Class Location Citations Comment
Metal-Binding-Site 5
UniProt: Zinc.
Metal-Binding-Site 8
UniProt: Zinc.
Metal-Binding-Site 21
UniProt: Zinc.
Metal-Binding-Site 25
UniProt: Zinc.
Amino-Acid-Sites-That-Bind 67
[Das04, UniProt15]
UniProt: S-adenosyl-L-methionine.
Protein-Segment 96 -> 97
UniProt: S-adenosyl-L-methionine binding; Sequence Annotation Type: region of interest;
Amino-Acid-Sites-That-Bind 183
[Das04, UniProt15]
UniProt: S-adenosyl-L-methionine.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1822 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG12207; 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

Bjork70: Bjork GR, Isaksson LA (1970). "Isolation of mutants of Escherichia coli lac king 5-methyluracil in transfer ribonucleic acid or 1-methylguanine in ribosomal RNA." J Mol Biol 51(1);83-100. PMID: 4921251

Bujnicki02a: Bujnicki JM, Blumenthal RM, Rychlewski L (2002). "Sequence analysis and structure prediction of 23S rRNA:m1G methyltransferases reveals a conserved core augmented with a putative Zn-binding domain in the N-terminus and family-specific elaborations in the C-terminus." J Mol Microbiol Biotechnol 4(1);93-9. PMID: 11763974

Das04: Das K, Acton T, Chiang Y, Shih L, Arnold E, Montelione GT (2004). "Crystal structure of RlmAI: implications for understanding the 23S rRNA G745/G748-methylation at the macrolide antibiotic-binding site." Proc Natl Acad Sci U S A 101(12);4041-6. PMID: 14999102

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

GOA01: GOA, MGI (2001). "Gene Ontology annotation based on Enzyme Commission mapping." Genomics 74;121-128.

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

Gustafsson98: Gustafsson C, Persson BC (1998). "Identification of the rrmA gene encoding the 23S rRNA m1G745 methyltransferase in Escherichia coli and characterization of an m1G745-deficient mutant." J Bacteriol 180(2);359-65. PMID: 9440525

Hansen01a: Hansen LH, Kirpekar F, Douthwaite S (2001). "Recognition of nucleotide G745 in 23 S ribosomal RNA by the rrmA methyltransferase." J Mol Biol 310(5);1001-10. PMID: 11501991

Isaksson73: Isaksson LA (1973). "Partial purification of ribosomal RNA(m1G)- and rRNA(m2G)-methylases from Escherichia coli and demonstration of some proteins affecting their apparent activity." Biochim Biophys Acta 312(1);122-33. PMID: 4580201

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

Liu02: Liu M, Douthwaite S (2002). "Methylation at nucleotide G745 or G748 in 23S rRNA distinguishes Gram-negative from Gram-positive bacteria." Mol Microbiol 44(1);195-204. PMID: 11967079

Liu04c: Liu M, Novotny GW, Douthwaite S (2004). "Methylation of 23S rRNA nucleotide G745 is a secondary function of the RlmAI methyltransferase." RNA 10(11);1713-20. PMID: 15388872

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

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

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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