ID   TRUD_PYRAB              Reviewed;         406 AA.
AC   Q9V107; G8ZJ87;
DT   26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-MAY-2000, sequence version 1.
DT   25-MAY-2022, entry version 106.
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=PYRAB06220;
GN   ORFNames=PAB0430;
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).
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; AJ248284; CAB49544.1; -; Genomic_DNA.
DR   EMBL; HE613800; CCE70014.1; -; Genomic_DNA.
DR   PIR; A75183; A75183.
DR   RefSeq; WP_010867746.1; NC_000868.1.
DR   AlphaFoldDB; Q9V107; -.
DR   SMR; Q9V107; -.
DR   STRING; 272844.PAB0430; -.
DR   EnsemblBacteria; CAB49544; CAB49544; PAB0430.
DR   GeneID; 1495527; -.
DR   KEGG; pab:PAB0430; -.
DR   PATRIC; fig|272844.11.peg.660; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   PhylomeDB; Q9V107; -.
DR   Proteomes; UP000000810; Chromosome.
DR   Proteomes; UP000009139; 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..406
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152549"
FT   DOMAIN          150..371
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        77
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   406 AA;  47544 MW;  0C9F6E9760345ADE CRC64;
     MLEELKYLSE TPGIGGRIKV KPEDFIVREI IPKSIFKGNC QIYLMKKRNW ETIAAIKEIA
     KRIGIHYSEI GFAGTKDRHA VTYQYISVCR DVRKEVEKLK IRDVELKFVG YGRPLKLGFL
     LGNFFLIRVR DVKRPELIPK IIEELKIKGG FPNYFGIQRF GEKRSVNHIV GKLLLEGKYE
     EAAEVFLGYP GNGMEGDEAR KRFLETKDVD LALEEFPKFL RYERAMLYRY RETRSWKKAF
     LVLPRPILRI FIHAFQAYLF NLYLSRRIEE GLPLNEAIPG DIVVQVKRGI PLRTRTYRVT
     ETNVDFVNEK IKRGEAMVSG PIFGYSYRKA HGIPGRLEEE ILDENEVNVE MFKKLPKPMR
     EPGGRRELLI KPRKFAYKRK EEEVLFKFFL PKGVYATSVL REITKH