TRMA_ECOLI
ID TRMA_ECOLI Reviewed; 366 AA.
AC P23003; Q2M8R0;
DT 01-AUG-1991, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1991, sequence version 1.
DT 03-AUG-2022, entry version 169.
DE RecName: Full=tRNA/tmRNA (uracil-C(5))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01011};
DE EC=2.1.1.- {ECO:0000255|HAMAP-Rule:MF_01011};
DE EC=2.1.1.35 {ECO:0000255|HAMAP-Rule:MF_01011};
DE AltName: Full=tRNA (uracil(54)-C(5))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01011};
DE AltName: Full=tRNA(m5U54)-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01011};
DE Short=RUMT {ECO:0000255|HAMAP-Rule:MF_01011};
DE AltName: Full=tmRNA (uracil(341)-C(5))-methyltransferase {ECO:0000255|HAMAP-Rule:MF_01011};
GN Name=trmA {ECO:0000255|HAMAP-Rule:MF_01011};
GN OrderedLocusNames=b3965, JW3937;
OS Escherichia coli (strain K12).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Enterobacteriaceae; Escherichia.
OX NCBI_TaxID=83333;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-18, AND REGULATION
RP OF TRANSCRIPTION.
RX PubMed=1999392; DOI=10.1128/jb.173.5.1757-1764.1991;
RA Gustafsson C., Lindstroem P.H.R., Hagervall T.G., Esberg K.B., Bjoerk G.R.;
RT "The trmA promoter has regulatory features and sequence elements in common
RT with the rRNA P1 promoter family of Escherichia coli.";
RL J. Bacteriol. 173:1757-1764(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=8265357; DOI=10.1093/nar/21.23.5408;
RA Blattner F.R., Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L.;
RT "Analysis of the Escherichia coli genome. IV. DNA sequence of the region
RT from 89.2 to 92.8 minutes.";
RL Nucleic Acids Res. 21:5408-5417(1993).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / MG1655 / ATCC 47076;
RX PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA Shao Y.;
RT "The complete genome sequence of Escherichia coli K-12.";
RL Science 277:1453-1462(1997).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX PubMed=16738553; DOI=10.1038/msb4100049;
RA Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT and W3110.";
RL Mol. Syst. Biol. 2:E1-E5(2006).
RN [5]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 353-366.
RC STRAIN=K12;
RX PubMed=1447162; DOI=10.1128/jb.174.23.7878-7879.1992;
RA Gustafsson C., Warne S.R.;
RT "Physical map of the oxyR-trmA region (minute 89.3) of the Escherichia coli
RT chromosome.";
RL J. Bacteriol. 174:7878-7879(1992).
RN [6]
RP FUNCTION.
RC STRAIN=K12;
RX PubMed=6247318; DOI=10.1128/jb.142.2.371-379.1980;
RA Ny T., Bjoerk G.R.;
RT "Cloning and restriction mapping of the trmA gene coding for transfer
RT ribonucleic acid (5-methyluridine)-methyltransferase in Escherichia coli K-
RT 12.";
RL J. Bacteriol. 142:371-379(1980).
RN [7]
RP FUNCTION.
RC STRAIN=K12;
RX PubMed=2999071; DOI=10.1128/jb.164.3.1117-1123.1985;
RA Lindstreom P.H.R., Stueber D., Bjoerk G.R.;
RT "Genetic organization and transcription from the gene (trmA) responsible
RT for synthesis of tRNA (uracil-5)-methyltransferase by Escherichia coli.";
RL J. Bacteriol. 164:1117-1123(1985).
RN [8]
RP IDENTIFICATION BY 2D-GEL.
RX PubMed=9298644; DOI=10.1002/elps.1150180805;
RA VanBogelen R.A., Abshire K.Z., Moldover B., Olson E.R., Neidhardt F.C.;
RT "Escherichia coli proteome analysis using the gene-protein database.";
RL Electrophoresis 18:1243-1251(1997).
RN [9]
RP FUNCTION AS A TMRNA METHYLTRANSFERASE, CATALYTIC ACTIVITY, AND DISRUPTION
RP PHENOTYPE.
RC STRAIN=K12 / BW25113;
RX PubMed=23603891; DOI=10.4161/rna.24327;
RA Ranaei-Siadat E., Fabret C., Seijo B., Dardel F., Grosjean H.,
RA Nonin-Lecomte S.;
RT "RNA-methyltransferase TrmA is a dual-specific enzyme responsible for C(5)-
RT methylation of uridine in both tmRNA and tRNA.";
RL RNA Biol. 10:572-578(2013).
RN [10]
RP X-RAY CRYSTALLOGRAPHY (2.43 ANGSTROMS) OF MUTANT GLN-358 IN A COVALENT
RP COMPLEX WITH A 19-NT T ARM ANALOG, MUTAGENESIS OF GLU-358, REACTION
RP MECHANISM, AND ACTIVE SITE.
RX PubMed=18451029; DOI=10.1073/pnas.0802247105;
RA Alian A., Lee T.T., Griner S.L., Stroud R.M., Finer-Moore J.;
RT "Structure of a TrmA-RNA complex: A consensus RNA fold contributes to
RT substrate selectivity and catalysis in m5U methyltransferases.";
RL Proc. Natl. Acad. Sci. U.S.A. 105:6876-6881(2008).
CC -!- FUNCTION: Dual-specificity methyltransferase that catalyzes the
CC formation of 5-methyluridine at position 54 (m5U54) in all tRNAs, and
CC that of position 341 (m5U341) in tmRNA (transfer-mRNA).
CC {ECO:0000255|HAMAP-Rule:MF_01011, ECO:0000269|PubMed:23603891,
CC ECO:0000269|PubMed:2999071, ECO:0000269|PubMed:6247318}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(54) in tRNA = 5-
CC methyluridine(54) in tRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:42712, Rhea:RHEA-COMP:10167, Rhea:RHEA-COMP:10193,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; EC=2.1.1.35;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_01011,
CC ECO:0000269|PubMed:23603891};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-adenosyl-L-methionine + uridine(341) in tmRNA = 5-
CC methyluridine(341) in tmRNA + H(+) + S-adenosyl-L-homocysteine;
CC Xref=Rhea:RHEA:43612, Rhea:RHEA-COMP:10630, Rhea:RHEA-COMP:10631,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:57856, ChEBI:CHEBI:59789,
CC ChEBI:CHEBI:65315, ChEBI:CHEBI:74447; Evidence={ECO:0000255|HAMAP-
CC Rule:MF_01011, ECO:0000269|PubMed:23603891};
CC -!- INDUCTION: Growth rate-dependent regulation of transcription. Is a
CC novel example of a mRNA regulated through a mechanism similar to that
CC of a stable RNA (rRNA).
CC -!- DISRUPTION PHENOTYPE: Cells lacking this gene exhibit a lack of m5U
CC modification in tmRNA. {ECO:0000269|PubMed:23603891}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. TrmA subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_01011}.
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DR EMBL; M57568; AAA24691.1; -; Genomic_DNA.
DR EMBL; U00006; AAC43071.1; -; Genomic_DNA.
DR EMBL; U00096; AAC76947.1; -; Genomic_DNA.
DR EMBL; AP009048; BAE77346.1; -; Genomic_DNA.
DR EMBL; X66026; CAA46825.1; -; Genomic_DNA.
DR PIR; A37321; A37321.
DR RefSeq; NP_418400.1; NC_000913.3.
DR RefSeq; WP_000187022.1; NZ_STEB01000037.1.
DR PDB; 3BT7; X-ray; 2.43 A; A/B=1-366.
DR PDBsum; 3BT7; -.
DR AlphaFoldDB; P23003; -.
DR SMR; P23003; -.
DR BioGRID; 4260659; 1.
DR DIP; DIP-11031N; -.
DR IntAct; P23003; 5.
DR STRING; 511145.b3965; -.
DR jPOST; P23003; -.
DR PaxDb; P23003; -.
DR PRIDE; P23003; -.
DR EnsemblBacteria; AAC76947; AAC76947; b3965.
DR EnsemblBacteria; BAE77346; BAE77346; BAE77346.
DR GeneID; 66672123; -.
DR GeneID; 947143; -.
DR KEGG; ecj:JW3937; -.
DR KEGG; eco:b3965; -.
DR PATRIC; fig|1411691.4.peg.2739; -.
DR EchoBASE; EB1015; -.
DR eggNOG; COG2265; Bacteria.
DR HOGENOM; CLU_043022_0_0_6; -.
DR InParanoid; P23003; -.
DR OMA; DHMESGV; -.
DR PhylomeDB; P23003; -.
DR BioCyc; EcoCyc:EG11022-MON; -.
DR BioCyc; MetaCyc:EG11022-MON; -.
DR BRENDA; 2.1.1.35; 2026.
DR EvolutionaryTrace; P23003; -.
DR PRO; PR:P23003; -.
DR Proteomes; UP000000318; Chromosome.
DR Proteomes; UP000000625; Chromosome.
DR GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR GO; GO:0019843; F:rRNA binding; IDA:EcoCyc.
DR GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; IDA:EcoCyc.
DR GO; GO:0000049; F:tRNA binding; IDA:EcoCyc.
DR GO; GO:0061818; P:tRNA folding; IDA:EcoCyc.
DR GO; GO:0030488; P:tRNA methylation; IMP:EcoCyc.
DR Gene3D; 3.40.50.150; -; 1.
DR HAMAP; MF_01011; RNA_methyltr_TrmA; 1.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
DR InterPro; IPR030391; MeTrfase_TrmA_CS.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR011869; TrmA_MeTrfase.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR47790; PTHR47790; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF53335; SSF53335; 1.
DR TIGRFAMs; TIGR02143; trmA_only; 1.
DR PROSITE; PS51687; SAM_MT_RNA_M5U; 1.
DR PROSITE; PS01230; TRMA_1; 1.
DR PROSITE; PS01231; TRMA_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Methyltransferase;
KW Reference proteome; S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..366
FT /note="tRNA/tmRNA (uracil-C(5))-methyltransferase"
FT /id="PRO_0000161859"
FT ACT_SITE 324
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011,
FT ECO:0000269|PubMed:18451029"
FT ACT_SITE 358
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011,
FT ECO:0000269|PubMed:18451029"
FT BINDING 190
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT BINDING 218
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT BINDING 223
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT BINDING 239
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT BINDING 299
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT SITE 190
FT /note="Interaction with RNA"
FT SITE 299
FT /note="Interaction with RNA"
FT SITE 302
FT /note="Interaction with RNA"
FT MUTAGEN 358
FT /note="E->Q: Loss of catalytic activity."
FT /evidence="ECO:0000269|PubMed:18451029"
FT HELIX 8..10
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 11..26
FT /evidence="ECO:0007829|PDB:3BT7"
FT TURN 27..29
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 35..37
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 41..43
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 45..55
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 58..64
FT /evidence="ECO:0007829|PDB:3BT7"
FT TURN 66..68
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 71..73
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 82..95
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 99..102
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 105..112
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 117..126
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 130..144
FT /evidence="ECO:0007829|PDB:3BT7"
FT TURN 145..147
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 149..156
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 159..164
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 166..171
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 180..184
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 193..206
FT /evidence="ECO:0007829|PDB:3BT7"
FT TURN 207..209
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 212..218
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 223..228
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 229..231
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 232..238
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 242..254
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 259..263
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 268..274
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 283..285
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 288..290
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 293..298
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 307..313
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 316..324
FT /evidence="ECO:0007829|PDB:3BT7"
FT HELIX 326..339
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 340..348
FT /evidence="ECO:0007829|PDB:3BT7"
FT STRAND 358..365
FT /evidence="ECO:0007829|PDB:3BT7"
SQ SEQUENCE 366 AA; 41967 MW; A7A65FD98380D27D CRC64;
MTPEHLPTEQ YEAQLAEKVV RLQSMMAPFS DLVPEVFRSP VSHYRMRAEF RIWHDGDDLY
HIIFDQQTKS RIRVDSFPAA SELINQLMTA MIAGVRNNPV LRHKLFQIDY LTTLSNQAVV
SLLYHKKLDD EWRQEAEALR DALRAQNLNV HLIGRATKTK IELDQDYIDE RLPVAGKEMI
YRQVENSFTQ PNAAMNIQML EWALDVTKGS KGDLLELYCG NGNFSLALAR NFDRVLATEI
AKPSVAAAQY NIAANHIDNV QIIRMAAEEF TQAMNGVREF NRLQGIDLKS YQCETIFVDP
PRSGLDSETE KMVQAYPRIL YISCNPETLC KNLETLSQTH KVERLALFDQ FPYTHHMECG
VLLTAK
