ID   TRUD_YERP3              Reviewed;         349 AA.
AC   A7FLX6;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   11-SEP-2007, sequence version 1.
DT   03-AUG-2022, entry version 78.
DE   RecName: Full=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};
GN   OrderedLocusNames=YpsIP31758_3297;
OS   Yersinia pseudotuberculosis serotype O:1b (strain IP 31758).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Yersiniaceae; Yersinia.
OX   NCBI_TaxID=349747;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=IP 31758;
RX   PubMed=17784789; DOI=10.1371/journal.pgen.0030142;
RA   Eppinger M., Rosovitz M.J., Fricke W.F., Rasko D.A., Kokorina G.,
RA   Fayolle C., Lindler L.E., Carniel E., Ravel J.;
RT   "The complete genome sequence of Yersinia pseudotuberculosis IP31758, the
RT   causative agent of Far East scarlet-like fever.";
RL   PLoS Genet. 3:1508-1523(2007).
CC   -!- FUNCTION: Responsible for synthesis of pseudouridine from uracil-13 in
CC       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; CP000720; ABS48455.1; -; Genomic_DNA.
DR   RefSeq; WP_011191777.1; NC_009708.1.
DR   AlphaFoldDB; A7FLX6; -.
DR   SMR; A7FLX6; -.
DR   EnsemblBacteria; ABS48455; ABS48455; YpsIP31758_3297.
DR   GeneID; 66842807; -.
DR   KEGG; ypi:YpsIP31758_3297; -.
DR   HOGENOM; CLU_005281_4_0_6; -.
DR   OMA; LWLWVEK; -.
DR   Proteomes; UP000002412; 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; 3.30.2340.10; -; 1.
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   InterPro; IPR043165; TruD_insert_sf.
DR   Pfam; PF01142; TruD; 2.
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..349
FT                   /note="tRNA pseudouridine synthase D"
FT                   /id="PRO_1000084770"
FT   DOMAIN          154..302
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        79
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   BINDING         26
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   BINDING         128
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   BINDING         328
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   349 AA;  39148 MW;  5D0D8CEC0977C29B CRC64;
     MDMENLTWLH GKPTASGILK ANPEDFVVVE DLGFEPDGEG EHLLVRIRKN GCNTQFVADY
     LARFAKLHPR LVSYAGLKDR HAVTEQWFCL HLPGKEAPDL ATFELEGCEV LEAVRHKRKL
     RIGSLKGNAF TLVLRHITDR QDVEQRLQQI AAQGVPNYFG SQRFGRGGNN LVQARLWANN
     EIRVKERSKR SFYLSASRSA MFNLISSHRL AQQLSTTVLE GDALQLSGRG SWFVAQADEL
     ATLQQRVTAG ELNITAPLPG DSELGTHGEA LAFEQACLAE QTELLSLIKR ERVEGSRRAV
     LLKPQNMISN WWDDVTLELS FWLPAGSFAT SVVREIMNQD RADDTDIIE