ID   TRUD_THEON              Reviewed;         416 AA.
AC   B6YTE4;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-JAN-2009, sequence version 1.
DT   25-MAY-2022, entry version 75.
DE   RecName: Full=Probable tRNA pseudouridine synthase D {ECO:0000255|HAMAP-Rule:MF_01082};
DE            EC=5.4.99.27 {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA pseudouridine(13) synthase {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA pseudouridylate synthase D {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA-uridine isomerase D {ECO:0000255|HAMAP-Rule:MF_01082};
GN   Name=truD {ECO:0000255|HAMAP-Rule:MF_01082}; OrderedLocusNames=TON_0346;
OS   Thermococcus onnurineus (strain NA1).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=523850;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=NA1;
RX   PubMed=18790866; DOI=10.1128/jb.00746-08;
RA   Lee H.S., Kang S.G., Bae S.S., Lim J.K., Cho Y., Kim Y.J., Jeon J.H.,
RA   Cha S.-S., Kwon K.K., Kim H.-T., Park C.-J., Lee H.-W., Kim S.I., Chun J.,
RA   Colwell R.R., Kim S.-J., Lee J.-H.;
RT   "The complete genome sequence of Thermococcus onnurineus NA1 reveals a
RT   mixed heterotrophic and carboxydotrophic metabolism.";
RL   J. Bacteriol. 190:7491-7499(2008).
CC   -!- FUNCTION: Could be responsible for synthesis of pseudouridine from
CC       uracil-13 in transfer RNAs. {ECO:0000255|HAMAP-Rule:MF_01082}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=uridine(13) in tRNA = pseudouridine(13) in tRNA;
CC         Xref=Rhea:RHEA:42540, Rhea:RHEA-COMP:10105, Rhea:RHEA-COMP:10106,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315; EC=5.4.99.27;
CC         Evidence={ECO:0000255|HAMAP-Rule:MF_01082};
CC   -!- SIMILARITY: Belongs to the pseudouridine synthase TruD family.
CC       {ECO:0000255|HAMAP-Rule:MF_01082}.
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DR   EMBL; CP000855; ACJ15831.1; -; Genomic_DNA.
DR   RefSeq; WP_012571303.1; NC_011529.1.
DR   AlphaFoldDB; B6YTE4; -.
DR   SMR; B6YTE4; -.
DR   STRING; 523850.TON_0346; -.
DR   EnsemblBacteria; ACJ15831; ACJ15831; TON_0346.
DR   GeneID; 7018009; -.
DR   KEGG; ton:TON_0346; -.
DR   PATRIC; fig|523850.10.peg.349; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   Proteomes; UP000002727; Chromosome.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0106029; F:tRNA pseudouridine synthase activity; IEA:UniProtKB-EC.
DR   GO; GO:0031119; P:tRNA pseudouridine synthesis; IEA:UniProtKB-UniRule.
DR   Gene3D; 3.30.2350.20; -; 1.
DR   HAMAP; MF_01082; TruD; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR001656; PsdUridine_synth_TruD.
DR   InterPro; IPR020119; PsdUridine_synth_TruD_CS.
DR   InterPro; IPR011760; PsdUridine_synth_TruD_insert.
DR   InterPro; IPR042214; TruD_catalytic.
DR   PANTHER; PTHR13326; PTHR13326; 1.
DR   Pfam; PF01142; TruD; 1.
DR   PIRSF; PIRSF037016; Pseudouridin_synth_euk_prd; 1.
DR   SUPFAM; SSF55120; SSF55120; 1.
DR   TIGRFAMs; TIGR00094; tRNA_TruD_broad; 1.
DR   PROSITE; PS50984; TRUD; 1.
DR   PROSITE; PS01268; UPF0024; 1.
PE   3: Inferred from homology;
KW   Isomerase; tRNA processing.
FT   CHAIN           1..416
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_1000136857"
FT   DOMAIN          158..379
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        83
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   416 AA;  48071 MW;  39AEA4A0B618970C CRC64;
     MDYREFFSQF KYLSEKPGIG GRIKAQPEDF IVMEEPLRSA FDGKKYAIFL LKKRNWDTMA
     AVKEIAKRAG ISYKDIGFAG TKDRHAVTYQ YISVPRDAKE KVEAVRIKDI ELRFVSYGRA
     LKLGHLLGNR FKIIVRDVDE SAFERTKEIV RELRSKGGFP NYFGYQRFGE RRVTNHLIGK
     LLLKGDFEGA ARLFLGAHGG GMEGDEARKN FWETGDVNRA LEEFPGFLRY ERAMLYRYKE
     TGSWRKAFLS LPLPIMRIFI HAYQSYLFNL YISRRIEEGL PLNEALVGDI VVQIKGGIPY
     RDRTYRVTET NIDFVKEKIR KDEAMVSGPL FGFSMRRARG VPGRLEEELL AEENLSLKDF
     KRLPKPMAEP GGRRELLIRP LGLTYGYVPS VGMCFRFFLP KGVYATSVLR EIMKDH