|Gene:||rlmA||Accession Numbers: EG12207 (EcoCyc), b1822, ECK1820|
Synonyms: rrmA, yebH, ribosomal RNA large subunit methyltransferase A, rRNA large subunit methyltransferase A
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 [Liu02g].
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 [Bujnicki02]. 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 [Liu04h].
RlmAI: "rRNA large subunit methyltransferase A" [Liu02g]
|Map Position: [1,904,275 <- 1,905,084] (41.04 centisomes)||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
In Paralogous Gene Group: 194 (13 members)
|Biological Process:||GO:0070475 - rRNA base methylation
GO:0006364 - rRNA processing [UniProtGOA11]
GO:0032259 - methylation [UniProtGOA11]
|Molecular Function:||GO:0008270 - zinc ion binding
GO:0008989 - rRNA (guanine-N1-)-methyltransferase activity [Hansen01a]
GO:0008168 - methyltransferase activity [UniProtGOA11, GOA01]
GO:0016740 - transferase activity [UniProtGOA11]
GO:0046872 - metal ion binding [UniProtGOA11]
GO:0052911 - 23S rRNA (guanine(745)-N(1))-methyltransferase activity [GOA01a]
|Cellular Component:||GO:0005737 - cytoplasm
GO:0005829 - cytosol [DiazMejia09]
|MultiFun Terms:||information transfer → RNA related → RNA modification|
|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]|
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: 18.104.22.168
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.
|Protein-Segment||96 -> 97|
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
Bujnicki02: 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
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
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
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