ID   TRUD_VIBVY              Reviewed;         347 AA.
AC   Q7MHQ6;
DT   16-JAN-2004, integrated into UniProtKB/Swiss-Prot.
DT   16-JAN-2004, sequence version 2.
DT   25-MAY-2022, entry version 100.
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}; OrderedLocusNames=VV2813;
OS   Vibrio vulnificus (strain YJ016).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC   Vibrio.
OX   NCBI_TaxID=196600;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=YJ016;
RX   PubMed=14656965; DOI=10.1101/gr.1295503;
RA   Chen C.-Y., Wu K.-M., Chang Y.-C., Chang C.-H., Tsai H.-C., Liao T.-L.,
RA   Liu Y.-M., Chen H.-J., Shen A.B.-T., Li J.-C., Su T.-L., Shao C.-P.,
RA   Lee C.-T., Hor L.-I., Tsai S.-F.;
RT   "Comparative genome analysis of Vibrio vulnificus, a marine pathogen.";
RL   Genome Res. 13:2577-2587(2003).
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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAC95577.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; BA000037; BAC95577.1; ALT_INIT; Genomic_DNA.
DR   RefSeq; WP_026130623.1; NC_005139.1.
DR   AlphaFoldDB; Q7MHQ6; -.
DR   SMR; Q7MHQ6; -.
DR   STRING; 672.VV93_v1c25230; -.
DR   EnsemblBacteria; BAC95577; BAC95577; BAC95577.
DR   KEGG; vvy:VV2813; -.
DR   PATRIC; fig|196600.6.peg.2803; -.
DR   eggNOG; COG0585; Bacteria.
DR   HOGENOM; CLU_005281_4_0_6; -.
DR   OMA; LWLWVEK; -.
DR   OrthoDB; 1490777at2; -.
DR   Proteomes; UP000002675; Chromosome I.
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; Reference proteome; tRNA processing.
FT   CHAIN           1..347
FT                   /note="tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152529"
FT   DOMAIN          158..304
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        81
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   347 AA;  38524 MW;  BA4A2FCB5336B7F4 CRC64;
     MTDTLASLAY LAGKPTAQAK IKAKPEHFQV REDLGFEFTG SGEHLMVRIR KTGENTSFVA
     NELAKACGVK SKDVSWAGLK DRHAVTEQWL SVHLPKAETP DFSAFLAQYP SIEILATARH
     NKKLRPGDLV GNDFVVTLSE VSDVDDVLKR LETVAKLGVP NYFGNQRFGN NGNNLQEAKR
     WGRDNVRSRN QNQRSLYLSA ARSWIFNLIV SARLEQSLFD KVLLGDILFK GDEQLLVSAE
     NHADLQSQYD AGDLVISGAL AGDNALPTQD DALALEQVFL DAEPDLMALI RGNRMRHDRR
     AIALKPANLS WQVDGNNIIL TFSLDAGSFA TSIIRELVQE IAFEREF