ID   TRUD_YERPN              Reviewed;         349 AA.
AC   Q1CLR4; C4GPS4;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   11-JUL-2006, sequence version 1.
DT   03-AUG-2022, entry version 87.
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=YPN_0734;
GN   ORFNames=YP516_0782;
OS   Yersinia pestis bv. Antiqua (strain Nepal516).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Yersiniaceae; Yersinia.
OX   NCBI_TaxID=377628;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Nepal516;
RX   PubMed=16740952; DOI=10.1128/jb.00124-06;
RA   Chain P.S.G., Hu P., Malfatti S.A., Radnedge L., Larimer F., Vergez L.M.,
RA   Worsham P., Chu M.C., Andersen G.L.;
RT   "Complete genome sequence of Yersinia pestis strains Antiqua and Nepal516:
RT   evidence of gene reduction in an emerging pathogen.";
RL   J. Bacteriol. 188:4453-4463(2006).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Nepal516;
RA   Plunkett G. III, Anderson B.D., Baumler D.J., Burland V., Cabot E.L.,
RA   Glasner J.D., Mau B., Neeno-Eckwall E., Perna N.T., Munk A.C., Tapia R.,
RA   Green L.D., Rogers Y.C., Detter J.C., Bruce D.C., Brettin T.S.;
RT   "Yersinia pestis Nepal516A whole genome shotgun sequencing project.";
RL   Submitted (APR-2009) to the EMBL/GenBank/DDBJ databases.
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; CP000305; ABG17066.1; -; Genomic_DNA.
DR   EMBL; ACNQ01000007; EEO77930.1; -; Genomic_DNA.
DR   RefSeq; WP_002209393.1; NZ_ACNQ01000007.1.
DR   AlphaFoldDB; Q1CLR4; -.
DR   SMR; Q1CLR4; -.
DR   EnsemblBacteria; ABG17066; ABG17066; YPN_0734.
DR   GeneID; 57975350; -.
DR   KEGG; ypn:YPN_0734; -.
DR   HOGENOM; CLU_005281_4_0_6; -.
DR   OMA; LWLWVEK; -.
DR   Proteomes; UP000008936; 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_1000084772"
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;  39144 MW;  41672651740EBBFE CRC64;
     MDMENLTWLH GKPTASGILK ANPEDFVVVE DLGFEPDGEG EHLLVRIRKN GCNTQFVADY
     LARFAKLHPR LVSYAGLKDR HAVTEQWFCL HLPGKEAPDL ATFELEGCEV LEAVRHKRKL
     RIGSLKGNAF TLVLRHITDR QDVEQRLQQI AAQGVPNYFG SQRFGRGGNN LVQARLWANN
     EIRVKERSKR SFYLSASRSA MFNLISSYRL AQQLSTTVLE GDALQLSGRG SWFVAQADEL
     AALQQRVTAG ELNITAPLPG DSELGTHGEA LAFEQACLAE QTELLSLIKR ERVEGSRRAV
     LLKPQNMISN WWDDVTLELS FWLPAGSFAT SVVREIMNQD RADDTDIIE