|Gene:||trmA||Accession Numbers: EG11022 (EcoCyc), b3965, ECK3957|
trmA encodes the methyltransferase that is responsible for methylation of U54 in all tRNAs. The enzyme is present in both a free form and strongly bound to tRNA and 16S rRNA in vivo, but is not associated with the ribosome [Gustafsson93].
The catalytic mechanism involves formation of a covalent complex between the catalytic Cys324 residue of the enzyme and tRNA [Santi87, Kealey91]. Random and site-directed mutagenesis of conserved residues allowed identification of residues involved in formation of the TrmA-tRNA intermediate and enzymatic activity [Urbonavicius07].
The trmA5 point mutant that lacks all m5U modification of tRNA has essentially no detectable phenotype, although it is outcompeted by wild type in mixed populations [Bjork75]. Introduction of the trmA5 to a double truB trmH mutant, resulting in lack of m5U54, ψ55, and Gm18 modifications to tRNA, only slightly worsens the growth rate defect of the truB trmH mutant [Urbonavicius02]. There are conflicting results concerning the essential nature of trmA: An earlier report suggested that the trmA gene is essential for viability, implying a second, vital function in addition to m5U modification of tRNA [Persson92], but trmA deletion strains were later obtained [Baba06].
Expression of trmA is growth rate-dependent [Gustafsson91].
TrmA: "transfer RNA methylation" [Bjork70]
|Map Position: [4,160,193 <- 4,161,293] (89.67 centisomes, 323°)||Length: 1101 bp / 366 aa|
Molecular Weight of Polypeptide: 41.967 kD (from nucleotide sequence), 42 kD (experimental) [Ny80 ]
pI: 4.7 [Ny88]
Unification Links: ASAP:ABE-0012983 , CGSC:79 , DIP:DIP-11031N , EchoBASE:EB1015 , EcoGene:EG11022 , EcoliWiki:b3965 , Mint:MINT-1223595 , ModBase:P23003 , OU-Microarray:b3965 , PortEco:trmA , Pride:P23003 , Protein Model Portal:P23003 , RefSeq:NP_418400 , RegulonDB:EG11022 , SMR:P23003 , String:511145.b3965 , UniProt:P23003
Relationship Links: InterPro:IN-FAMILY:IPR010280 , InterPro:IN-FAMILY:IPR011869 , InterPro:IN-FAMILY:IPR029063 , InterPro:IN-FAMILY:IPR030390 , InterPro:IN-FAMILY:IPR030391 , PDB:Structure:3BT7 , Pfam:IN-FAMILY:PF05958 , Prosite:IN-FAMILY:PS01230 , Prosite:IN-FAMILY:PS01231 , Prosite:IN-FAMILY:PS51687
In Paralogous Gene Group: 217 (3 members)
|Biological Process:||GO:0030488 - tRNA methylation
GO:0006396 - RNA processing [GOA01a]
GO:0008033 - tRNA processing [UniProtGOA11a]
GO:0032259 - methylation [UniProtGOA11a]
|Molecular Function:||GO:0000049 - tRNA binding
GO:0019843 - rRNA binding [Gustafsson93]
GO:0030697 - S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity [GOA06, GOA01, GOA01a, Greenberg80]
GO:0008168 - methyltransferase activity [UniProtGOA11a]
GO:0008173 - RNA methyltransferase activity [GOA01a]
GO:0016740 - transferase activity [UniProtGOA11a]
|Cellular Component:||GO:0005829 - cytosol
[DiazMejia09, Ishihama08, LopezCampistrou05]
GO:0005737 - cytoplasm
|MultiFun Terms:||information transfer → RNA related → RNA modification|
|Growth Medium||Growth?||T (°C)||O2||pH||Osm/L||Growth Observations|
|LB enriched||Yes||37||Aerobic||6.95||Yes [Gerdes03, Comment 1]|
Enzymatic reaction of: tRNA(m5U54)methyltransferase (tRNA m5U54 methyltransferase)
Synonyms: tRNA (5-methyluridine)-methyltransferase, RUMT, tRNA (uracil-5-)-methyltransferase
EC Number: 22.214.171.124
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.
pH(opt): 8.4 [Greenberg80]
|Feature Class||Location||Common Name||Citations||Comment|
10/20/97 Gene b3965 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG11022; confirmed by SwissProt match.
Alian08: Alian A, Lee TT, Griner SL, Stroud RM, Finer-Moore J (2008). "Structure of a TrmA-RNA complex: A consensus RNA fold contributes to substrate selectivity and catalysis in m5U methyltransferases." Proc Natl Acad Sci U S A 105(19);6876-81. PMID: 18451029
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
Bjork75: Bjork GR, Neidhardt FC (1975). "Physiological and biochemical studies on the function of 5-methyluridine in the transfer ribonucleic acid of Escherichia coli." J Bacteriol 124(1);99-111. PMID: 1100618
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
Gustafsson91: Gustafsson C, Lindstrom PH, Hagervall TG, Esberg KB, Bjork GR (1991). "The trmA promoter has regulatory features and sequence elements in common with the rRNA P1 promoter family of Escherichia coli." J Bacteriol 173(5);1757-64. PMID: 1999392
Gustafsson93: Gustafsson C, Bjork GR (1993). "The tRNA-(m5U54)-methyltransferase of Escherichia coli is present in two forms in vivo, one of which is present as bound to tRNA and to a 3'-end fragment of 16 S rRNA." J Biol Chem 268(2);1326-31. PMID: 8419334
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
Ny80: Ny T, Bjork GR (1980). "Cloning and restriction mapping of the trmA gene coding for transfer ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-12." J Bacteriol 142(2);371-9. PMID: 6247318
Ny88: Ny T, Lindstrom HR, Hagervall TG, Bjork GR (1988). "Purification of transfer RNA (m5U54)-methyltransferase from Escherichia coli. Association with RNA." Eur J Biochem 177(3);467-75. PMID: 2461858
Persson92: Persson BC, Gustafsson C, Berg DE, Bjork GR (1992). "The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli." Proc Natl Acad Sci U S A 89(9);3995-8. PMID: 1373891
Urbonavicius02: Urbonavicius J, Durand JM, Bjork GR (2002). "Three modifications in the D and T arms of tRNA influence translation in Escherichia coli and expression of virulence genes in Shigella flexneri." J Bacteriol 184(19);5348-57. PMID: 12218021
Urbonavicius07: Urbonavicius J, Jager G, Bjork GR (2007). "Amino acid residues of the Escherichia coli tRNA(m5U54)methyltransferase (TrmA) critical for stability, covalent binding of tRNA and enzymatic activity." Nucleic Acids Res 35(10):3297-305. PMID: 17459887
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