ID   TRUD_PYRHO              Reviewed;         409 AA.
AC   O59207;
DT   26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-AUG-1998, sequence version 1.
DT   25-MAY-2022, entry version 112.
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=PH1538;
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: 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; BA000001; BAA30648.1; -; Genomic_DNA.
DR   PIR; H71030; H71030.
DR   RefSeq; WP_010885615.1; NC_000961.1.
DR   AlphaFoldDB; O59207; -.
DR   SMR; O59207; -.
DR   STRING; 70601.3257965; -.
DR   EnsemblBacteria; BAA30648; BAA30648; BAA30648.
DR   GeneID; 1443855; -.
DR   KEGG; pho:PH1538; -.
DR   eggNOG; arCOG04252; Archaea.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   Proteomes; UP000000752; 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..409
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152552"
FT   DOMAIN          152..373
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        82
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   409 AA;  47233 MW;  A5D14085DD5DFA97 CRC64;
     MLEDPLRNLR YLTSSPGIGG KIKVYPEDFI VKEVIPKSIF RGGRCRIYLL KKKNWETMAA
     IKEIAKRIGI HYSEIGFAGT KDRHAVTYQY ISICREVDLE NVAIKDVTLR FVGYGRPLKL
     GLLLGNFFKI RVRDTTPELL PNILKEAKEK GGFPNYFGIQ RFGEKRSVNH IVGKLLLLGK
     YEEAAEVFLG YPGNGMEGDE ARKKFLETKN VDLALEEFPK FLRYERAMLY KYRETGSWKR
     SFLALPRPIL RIFIHAFQSY LFNLYISRRI EEGFPLNEAL PGDIVVQVKK GIPLRDRTYR
     VTESNLDFVN EKIMQGEAMV SGPIFGYSYR RSHGIPGRLE DEILEEAGVS LENFKRLPKP
     MREPGGRREL LIKPRGFRYK TEGRDVLFKF FLPKGVYATS VLREIIKPT