ATRMA_PYRAB
ID ATRMA_PYRAB Reviewed; 405 AA.
AC Q9UZR7; G8ZJN0;
DT 19-JUL-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 116.
DE RecName: Full=tRNA (uracil(54)-C(5))-methyltransferase;
DE EC=2.1.1.35;
DE AltName: Full=PabTrmU54;
DE AltName: Full=tRNA(m5U54)-methyltransferase;
DE Short=RUMT;
GN OrderedLocusNames=PYRAB10780; ORFNames=PAB0719;
OS Pyrococcus abyssi (strain GE5 / Orsay).
OC Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC Pyrococcus.
OX NCBI_TaxID=272844;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=GE5 / Orsay;
RX PubMed=12622808; DOI=10.1046/j.1365-2958.2003.03381.x;
RA Cohen G.N., Barbe V., Flament D., Galperin M., Heilig R., Lecompte O.,
RA Poch O., Prieur D., Querellou J., Ripp R., Thierry J.-C., Van der Oost J.,
RA Weissenbach J., Zivanovic Y., Forterre P.;
RT "An integrated analysis of the genome of the hyperthermophilic archaeon
RT Pyrococcus abyssi.";
RL Mol. Microbiol. 47:1495-1512(2003).
RN [2]
RP GENOME REANNOTATION.
RC STRAIN=GE5 / Orsay;
RX PubMed=22057919; DOI=10.1007/s00284-011-0035-x;
RA Gao J., Wang J.;
RT "Re-annotation of two hyperthermophilic archaea Pyrococcus abyssi GE5 and
RT Pyrococcus furiosus DSM 3638.";
RL Curr. Microbiol. 64:118-129(2012).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, IRON-SULFUR CLUSTER, AND
RP DOMAIN.
RX PubMed=18069966; DOI=10.1111/j.1365-2958.2007.06047.x;
RA Urbonavicius J., Auxilien S., Walbott H., Trachana K.,
RA Golinelli-Pimpaneau B., Brochier-Armanet C., Grosjean H.;
RT "Acquisition of a bacterial RumA-type tRNA(uracil-54, C5)-methyltransferase
RT by Archaea through an ancient horizontal gene transfer.";
RL Mol. Microbiol. 67:323-335(2008).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.80 ANGSTROMS) IN COMPLEX WITH
RP S-ADENOSYL-L-HOMOCYSTEINE, AND DOMAIN.
RX PubMed=18653523; DOI=10.1093/nar/gkn437;
RA Walbott H., Leulliot N., Grosjean H., Golinelli-Pimpaneau B.;
RT "The crystal structure of Pyrococcus abyssi tRNA (uracil-54, C5)-
RT methyltransferase provides insights into its tRNA specificity.";
RL Nucleic Acids Res. 36:4929-4940(2008).
CC -!- FUNCTION: Catalyzes the formation of 5-methyl-uridine at position 54
CC (m5U54) in tRNA. {ECO:0000269|PubMed:18069966}.
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:0000269|PubMed:18069966};
CC -!- ACTIVITY REGULATION: Activated by magnesium ions.
CC {ECO:0000269|PubMed:18069966}.
CC -!- DOMAIN: Contains a N-terminal TRAM-like domain, an iron-sulfur cluster
CC in the central region and a C-terminal catalytic domain. The tRNA-
CC binding site is probably formed at the interface of the three regions.
CC {ECO:0000269|PubMed:18069966, ECO:0000269|PubMed:18653523}.
CC -!- SIMILARITY: Belongs to the class I-like SAM-binding methyltransferase
CC superfamily. RNA M5U methyltransferase family. {ECO:0000255|PROSITE-
CC ProRule:PRU01024}.
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DR EMBL; AJ248286; CAB49989.1; -; Genomic_DNA.
DR EMBL; HE613800; CCE70489.1; -; Genomic_DNA.
DR PIR; H75085; H75085.
DR RefSeq; WP_010868196.1; NC_000868.1.
DR PDB; 2JJQ; X-ray; 1.80 A; A=1-405.
DR PDB; 2VS1; X-ray; 2.10 A; A=1-405.
DR PDBsum; 2JJQ; -.
DR PDBsum; 2VS1; -.
DR AlphaFoldDB; Q9UZR7; -.
DR SMR; Q9UZR7; -.
DR STRING; 272844.PAB0719; -.
DR PRIDE; Q9UZR7; -.
DR EnsemblBacteria; CAB49989; CAB49989; PAB0719.
DR GeneID; 1496434; -.
DR KEGG; pab:PAB0719; -.
DR PATRIC; fig|272844.11.peg.1133; -.
DR eggNOG; arCOG00122; Archaea.
DR HOGENOM; CLU_014689_8_1_2; -.
DR OMA; FYAGDMK; -.
DR OrthoDB; 25398at2157; -.
DR PhylomeDB; Q9UZR7; -.
DR BRENDA; 2.1.1.35; 5242.
DR EvolutionaryTrace; Q9UZR7; -.
DR Proteomes; UP000000810; Chromosome.
DR Proteomes; UP000009139; 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; IDA:UniProtKB.
DR GO; GO:0030488; P:tRNA methylation; IDA:UniProtKB.
DR Gene3D; 2.40.50.140; -; 1.
DR Gene3D; 3.40.50.150; -; 1.
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; 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 1: Evidence at protein level;
KW 3D-structure; 4Fe-4S; Iron; Iron-sulfur; Metal-binding; Methyltransferase;
KW S-adenosyl-L-methionine; Transferase; tRNA processing.
FT CHAIN 1..405
FT /note="tRNA (uracil(54)-C(5))-methyltransferase"
FT /id="PRO_0000162053"
FT ACT_SITE 367
FT /note="Nucleophile"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01024"
FT ACT_SITE 399
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 252
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 278
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 283
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 299..300
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 326
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT BINDING 340
FT /ligand="S-adenosyl-L-methionine"
FT /ligand_id="ChEBI:CHEBI:59789"
FT STRAND 2..4
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 14..16
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 19..21
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 29..51
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 71..74
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 77..92
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 97..99
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 104..106
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 110..116
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 130..133
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 138..140
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 142..158
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 162..164
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 165..168
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 171..179
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 181..183
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 186..195
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 201..203
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 207..213
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 216..218
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 224..230
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 234..238
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 241..245
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 255..268
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 271..277
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 280..282
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 283..290
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 294..300
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 302..315
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 319..323
FT /evidence="ECO:0007829|PDB:2JJQ"
FT TURN 326..328
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 335..339
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 348..357
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 360..367
FT /evidence="ECO:0007829|PDB:2JJQ"
FT HELIX 369..378
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 382..389
FT /evidence="ECO:0007829|PDB:2JJQ"
FT STRAND 399..405
FT /evidence="ECO:0007829|PDB:2JJQ"
SQ SEQUENCE 405 AA; 46849 MW; B17A8697DB04A881 CRC64;
MRGVIRKLND DGFGVLKGIL VPFSAPGDEI IVERVERVKK RRVASQWKLV RSSPLRVGPR
CKAFGKCGGC TLQHLNYDYQ LEFKRKKLKR ILGFEVEVVP SPKIFGHRNR IDLAITKDGI
GFRERGKWWK IVDIDECPVF GKTSREAIER LKEFIEEEKI SVWNIKKDEG FLRYMVLREG
KFTEEVMVNF VTKEGNLPDP TNYFDFDSIY WSVNRSKSDV SYGDIERFWG KEFIRERLDD
VDYLIHPNSF FQTNSYQAVN LVRKVSELVE GEKILDMYSG VGTFGIYLAK RGFNVKGFDS
NEFAIEMARR NVEINNVDAE FEVASDREVS VKGFDTVIVD PPRAGLHPRL VKRLNREKPG
VIVYVSCNPE TFARDVKMLD YRIDEIVALD MFPHTPHVEL VAKLV
