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TRMA_SHEWM
ID   TRMA_SHEWM              Reviewed;         365 AA.
AC   B1KN03;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   29-APR-2008, sequence version 1.
DT   03-AUG-2022, entry version 83.
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}; OrderedLocusNames=Swoo_4710;
OS   Shewanella woodyi (strain ATCC 51908 / MS32).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=392500;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 51908 / MS32;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA   Bruce D., Goodwin L., Pitluck S., Sims D., Brettin T., Detter J.C., Han C.,
RA   Kuske C.R., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA   Lykidis A., Zhao J.-S., Richardson P.;
RT   "Complete sequence of Shewanella woodyi ATCC 51908.";
RL   Submitted (FEB-2008) to the EMBL/GenBank/DDBJ databases.
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}.
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   -!- 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};
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; CP000961; ACA88960.1; -; Genomic_DNA.
DR   RefSeq; WP_012327278.1; NC_010506.1.
DR   AlphaFoldDB; B1KN03; -.
DR   SMR; B1KN03; -.
DR   STRING; 392500.Swoo_4710; -.
DR   EnsemblBacteria; ACA88960; ACA88960; Swoo_4710.
DR   KEGG; swd:Swoo_4710; -.
DR   eggNOG; COG2265; Bacteria.
DR   HOGENOM; CLU_043022_0_0_6; -.
DR   OMA; DHMESGV; -.
DR   OrthoDB; 1421660at2; -.
DR   Proteomes; UP000002168; Chromosome.
DR   GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; IEA:UniProtKB-UniRule.
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   3: Inferred from homology;
KW   Methyltransferase; Reference proteome; S-adenosyl-L-methionine;
KW   Transferase; tRNA processing.
FT   CHAIN           1..365
FT                   /note="tRNA/tmRNA (uracil-C(5))-methyltransferase"
FT                   /id="PRO_1000198558"
FT   ACT_SITE        323
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT   ACT_SITE        357
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT   BINDING         189
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT   BINDING         217
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT   BINDING         222
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT   BINDING         238
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
FT   BINDING         298
FT                   /ligand="S-adenosyl-L-methionine"
FT                   /ligand_id="ChEBI:CHEBI:59789"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01011"
SQ   SEQUENCE   365 AA;  42317 MW;  7E83871CA75A1B0D CRC64;
     MNLAAMDPNT YDAQLEEKRI KLENIFTDFD TPNLEVFSSE QAHYRMRAEF RIWHDGEDMY
     YYMFDKALNS KVRCDQFLPA SKLINEMMPA LIAELKPNPL LRHRLFQIDF LSTLSGEILV
     SLLYHKQLDE QWETEAKSLK ERLASKFNVN IIGRARKQKL IFDKDFVVES LQVNGEQLQY
     HQIENSFTQP NGKVSVKMLE WAIDVTKNSS GDLLELYCGN GNFSIALAQN FDRVLATELA
     KPSVESAQYN IKINKIDNLQ IIRMSAEDFT DAMAKKRSFR RLEGIDLDSY NCNTIFVDPP
     RAGMDPDTVK LVQGYERIVY ISCNPNTLID NLVELSKTHK ITRFALFDQF PYTDHMESGV
     FLERK
 
 
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