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TRMA_SHEDO
ID   TRMA_SHEDO              Reviewed;         365 AA.
AC   Q12SP8;
DT   20-MAR-2007, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   03-AUG-2022, entry version 91.
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=Sden_0231;
OS   Shewanella denitrificans (strain OS217 / ATCC BAA-1090 / DSM 15013).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=318161;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=OS217 / ATCC BAA-1090 / DSM 15013;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA   Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA   Brettin T., Bruce D., Han C., Tapia R., Gilna P., Kiss H., Schmutz J.,
RA   Larimer F., Land M., Hauser L., Kyrpides N., Lykidis A., Richardson P.;
RT   "Complete sequence of Shewanella denitrificans OS217.";
RL   Submitted (MAR-2006) 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; CP000302; ABE53528.1; -; Genomic_DNA.
DR   RefSeq; WP_011494695.1; NC_007954.1.
DR   AlphaFoldDB; Q12SP8; -.
DR   SMR; Q12SP8; -.
DR   STRING; 318161.Sden_0231; -.
DR   EnsemblBacteria; ABE53528; ABE53528; Sden_0231.
DR   KEGG; sdn:Sden_0231; -.
DR   eggNOG; COG2265; Bacteria.
DR   HOGENOM; CLU_043022_0_0_6; -.
DR   OMA; DHMESGV; -.
DR   OrthoDB; 1421660at2; -.
DR   Proteomes; UP000001982; 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_0000281459"
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;  41903 MW;  573CA7C2C2E993E6 CRC64;
     MNLAAMDPSN YDAQLAEKKR KLSEGFAEFA PPELEVFASE PAHYRMRAEF RVWHEGDDLY
     YYMFDKVLDA KVRCEQYLPA STLINAIMTS LVEELRPNHS LRHRLFQVDF LSTLSGEILV
     SLLYHRQLDE QWQVEAAALK QRLSSQFNVN IIGRARKQKI DLDKDFVVET IKVNGQDLHY
     KQIENSFTQP NAKVSIKMLE WAIDATKQSQ GDLLELYCGN GNFTIALAQN FNRVLATELA
     KPSVGAAQYN IAINNVDNVQ IIRMSAEDFS DAMAKKRSFR RLEGIDLDSY NCNTIFVDPP
     RAGIDDETLK LIQGYERILY ISCNPETLKD NLQTLSSSHK ITRFALFDQF PYTHHMESGV
     LLERK
 
 
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