Escherichia coli K-12 substr. MG1655 Enzyme: tRNA m5U54 methyltransferase

Gene: trmA Accession Numbers: EG11022 (EcoCyc), b3965, ECK3957

Synonyms: rT

Regulation Summary Diagram: ?

Regulation summary diagram for trmA

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]

Locations: cytosol

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)

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for trmA

GO Terms:

Biological Process: GO:0030488 - tRNA methylation Inferred from experiment Inferred by computational analysis [GOA06, Bjork75]
GO:0006396 - RNA processing Inferred by computational analysis [GOA01a]
GO:0008033 - tRNA processing Inferred by computational analysis [UniProtGOA11a]
GO:0032259 - methylation Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0000049 - tRNA binding Inferred from experiment [Gustafsson93]
GO:0019843 - rRNA binding Inferred from experiment [Gustafsson93]
GO:0030697 - S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity Inferred from experiment Inferred by computational analysis [GOA06, GOA01, GOA01a, Greenberg80]
GO:0008168 - methyltransferase activity Inferred by computational analysis [UniProtGOA11a]
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

MultiFun Terms: information transfer RNA related RNA modification

Essentiality data for trmA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]

Last-Curated ? 03-May-2007 by Keseler I , SRI International

Enzymatic reaction of: tRNA(m5U54)methyltransferase (tRNA m5U54 methyltransferase)

Synonyms: tRNA (5-methyluridine)-methyltransferase, RUMT, tRNA (uracil-5-)-methyltransferase

EC Number:

a uracil54 in tRNA + S-adenosyl-L-methionine <=> a 5-methyluracil54 in tRNA + 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.

Activators (Unknown Mechanism): Mg2+ [Ny88]

Kinetic Parameters:

Km (μM)
a uracil54 in tRNA

pH(opt): 8.4 [Greenberg80]

Sequence Features

Protein sequence of tRNA m5U54 methyltransferase with features indicated

Feature Class Location Common Name Citations Comment
Amino-Acid-Sites-That-Bind 190  
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 218  
UniProt: S-adenosyl-L-methionine; via carbonyl oxygen; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 223  
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 239  
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Sites-That-Bind 299  
UniProt: S-adenosyl-L-methionine; Non-Experimental Qualifier: by similarity;
Amino-Acid-Site 302  
UniProt: Interaction with RNA; Sequence Annotation Type: site.
Active-Site 324 catalytic nucleophile
[Alian08, Kealey91]
Mutagenesis-Variant 358  
[Alian08, UniProt14]
UniProt: Loss of catalytic activity.
Active-Site 358  
[Alian08, UniProt14]
UniProt: Proton acceptor.

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


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

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."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

Greenberg80: Greenberg R, Dudock B (1980). "Isolation and chracterization of m5U-methyltransferase from Escherichia coli." J Biol Chem 255(17);8296-302. PMID: 6997293

Gu90: Gu XR, Santi DV (1990). "High-level expression of Escherichia coli tRNA (m5U54)-methyltransferase." DNA Cell Biol 9(4);273-8. PMID: 2190591

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

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

Kealey91: Kealey JT, Santi DV (1991). "Identification of the catalytic nucleophile of tRNA (m5U54)methyltransferase." Biochemistry 30(40);9724-8. PMID: 1911760

Kealey94: Kealey JT, Santi DV (1994). "High-level expression and rapid purification of tRNA (m5U54)-methyltransferase." Protein Expr Purif 5(2);149-52. PMID: 8054847

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

Santi87: Santi DV, Hardy LW (1987). "Catalytic mechanism and inhibition of tRNA (uracil-5-)methyltransferase: evidence for covalent catalysis." Biochemistry 26(26);8599-606. PMID: 3327525

UniProt10: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt14: UniProt Consortium (2014). "UniProt version 2014-01 released on 2014-01-01 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."

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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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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