ID   TRUD_THEKO              Reviewed;         416 AA.
AC   Q5JDB6;
DT   26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT   15-FEB-2005, sequence version 1.
DT   25-MAY-2022, entry version 88.
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=TK2302;
OS   Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
OS   (Pyrococcus kodakaraensis (strain KOD1)).
OC   Archaea; Euryarchaeota; Thermococci; Thermococcales; Thermococcaceae;
OC   Thermococcus.
OX   NCBI_TaxID=69014;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC BAA-918 / JCM 12380 / KOD1;
RX   PubMed=15710748; DOI=10.1101/gr.3003105;
RA   Fukui T., Atomi H., Kanai T., Matsumi R., Fujiwara S., Imanaka T.;
RT   "Complete genome sequence of the hyperthermophilic archaeon Thermococcus
RT   kodakaraensis KOD1 and comparison with Pyrococcus genomes.";
RL   Genome Res. 15:352-363(2005).
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; AP006878; BAD86491.1; -; Genomic_DNA.
DR   RefSeq; WP_011251252.1; NC_006624.1.
DR   AlphaFoldDB; Q5JDB6; -.
DR   SMR; Q5JDB6; -.
DR   STRING; 69014.TK2302; -.
DR   PRIDE; Q5JDB6; -.
DR   EnsemblBacteria; BAD86491; BAD86491; TK2302.
DR   GeneID; 3233719; -.
DR   KEGG; tko:TK2302; -.
DR   PATRIC; fig|69014.16.peg.2257; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   InParanoid; Q5JDB6; -.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   PhylomeDB; Q5JDB6; -.
DR   Proteomes; UP000000536; Chromosome.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0106029; F:tRNA pseudouridine synthase activity; IEA:UniProtKB-EC.
DR   GO; GO:0001522; P:pseudouridine synthesis; IBA:GO_Central.
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; Reference proteome; tRNA processing.
FT   CHAIN           1..416
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152553"
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;  48538 MW;  E881A70B871AD24F CRC64;
     MDYREFFSQF KHLSEKPGIG GKIKIYPEDF IVIEEPIPSI FEGRKYAIFL LKKRNWETMA
     AVKEIAKRAG INYREIGFAG TKDRHAVTYQ YISVPAEARE RVEQVSIRDI ELRFVSYGRF
     IKLGHLLGNR FRIIVRDVSE DAFDRTKEIV RELREKGGFP NYFGYQRFGE RRVVNHIIGK
     LLLQGDFEGA ARLFLGAHDG SMEGDEARKN FWETGDVERA LEEFPGFLRY ERTLLHRYKD
     TGNWKRAFLS LPLPIMRIFI HAYQSYLFNL YLSRRIEEGL PLNEPLVGDI VVQVKGGIPY
     RDRTYRVTET NLEFVREKVR KNQAMVSGPL FGFAMRRAKG LPGELEKEIL EEEGLSLETF
     RRLPKPMAEP GGRRELLLRP MGMAYGYIQE EGMCFRFFLP KGTYATSVLR EIMKDH