ATRMA_PYRHO
ID ATRMA_PYRHO Reviewed; 407 AA.
AC O58864;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-AUG-1998, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=tRNA (uracil(54)-C(5))-methyltransferase;
DE EC=2.1.1.35;
DE AltName: Full=tRNA(m5U54)-methyltransferase;
DE Short=RUMT;
GN OrderedLocusNames=PH1137;
OS Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC
OS 100139 / OT-3).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=70601;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3;
RX PubMed=9679194; DOI=10.1093/dnares/5.2.55;
RA Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S.,
RA Sekine M., Baba S., Kosugi H., Hosoyama A., Nagai Y., Sakai M., Ogura K.,
RA Otsuka R., Nakazawa H., Takamiya M., Ohfuku Y., Funahashi T., Tanaka T.,
RA Kudoh Y., Yamazaki J., Kushida N., Oguchi A., Aoki K., Yoshizawa T.,
RA Nakamura Y., Robb F.T., Horikoshi K., Masuchi Y., Shizuya H., Kikuchi H.;
RT "Complete sequence and gene organization of the genome of a hyper-
RT thermophilic archaebacterium, Pyrococcus horikoshii OT3.";
RL DNA Res. 5:55-76(1998).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 54
CC (m5U54) in tRNA. {ECO:0000250}.
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 -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01024}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; BA000001; BAA30237.1; -; Genomic_DNA.
DR PIR; C71055; C71055.
DR RefSeq; WP_010885221.1; NC_000961.1.
DR AlphaFoldDB; O58864; -.
DR SMR; O58864; -.
DR STRING; 70601.3257554; -.
DR EnsemblBacteria; BAA30237; BAA30237; BAA30237.
DR GeneID; 1443456; -.
DR KEGG; pho:PH1137; -.
DR eggNOG; arCOG00122; Archaea.
DR OMA; FYAGDMK; -.
DR OrthoDB; 25398at2157; -.
DR Proteomes; UP000000752; Chromosome.
DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0030697; F:S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity; ISS:UniProtKB.
DR GO; GO:0030488; P:tRNA methylation; ISS:UniProtKB.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
DR InterPro; IPR030382; MeTrfase_TRM5/TYW2.
DR InterPro; IPR030390; MeTrfase_TrmA_AS.
DR InterPro; IPR030391; MeTrfase_TrmA_CS.
DR InterPro; IPR012340; NA-bd_OB-fold.
DR InterPro; IPR029063; SAM-dependent_MTases_sf.
DR InterPro; IPR010280; U5_MeTrfase_fam.
DR PANTHER; PTHR11061; PTHR11061; 1.
DR Pfam; PF02475; Met_10; 1.
DR Pfam; PF05958; tRNA_U5-meth_tr; 1.
DR SUPFAM; SSF53335; SSF53335; 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 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..407
FT /note="tRNA (uracil(54)-C(5))-methyltransferase"
FT /id="PRO_0000162057"
FT ACT_SITE 368
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT ACT_SITE 400
FT /note="Proton acceptor"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10015"
FT BINDING 61
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 67
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 70
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 137
FT /ligand="[4Fe-4S] cluster"
FT /ligand_id="ChEBI:CHEBI:49883"
FT /evidence="ECO:0000250"
FT BINDING 253
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 279
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 284
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 300..301
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000250"
FT BINDING 327
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT BINDING 341
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
SQ SEQUENCE 407 AA; 46490 MW; AA3D40A21D6ED216 CRC64;
MRGVVKELND DGFGVLGNVL VPFSAPGDEV EILKIEKVKK AKIASKWKLI KSSPLRVGAR
CKVFGRCGGC SLQHLSYDYQ LEFKGERIRR LLGVDVEVIP SPRIFGHRNR IDLAVTVEGI
GFRERGKWWK IVDIQECPVF GKTSRKAIER LREFIEEERI SVWNVKKDEG FLRYMVLREG
KFTGEVMVNL VTKEGKLPDP SKYFDFATSI YWSVNRTKSD VSYGEVESVW GREFITEKLD
DVIYLIHPNS FFQTNSYQAV NLVKKVSELV EGERVLDMYS GVGTFGIYLA KRGFKVVGFD
SNEFAIEMAR KNAKINKVDA VFDVATDREV EVNGFDTVIV DPPRVGLHPK LIKKLNREKP
EVIVYVSCNP KTFARDIEKL EYKIDEIVAL DMFPHTPHLE LVAKLIV
