ID   TRUD_SHISS              Reviewed;         349 AA.
AC   Q3YYB7;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   27-SEP-2005, 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=SSON_2893;
OS   Shigella sonnei (strain Ss046).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Shigella.
OX   NCBI_TaxID=300269;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=Ss046;
RX   PubMed=16275786; DOI=10.1093/nar/gki954;
RA   Yang F., Yang J., Zhang X., Chen L., Jiang Y., Yan Y., Tang X., Wang J.,
RA   Xiong Z., Dong J., Xue Y., Zhu Y., Xu X., Sun L., Chen S., Nie H., Peng J.,
RA   Xu J., Wang Y., Yuan Z., Wen Y., Yao Z., Shen Y., Qiang B., Hou Y., Yu J.,
RA   Jin Q.;
RT   "Genome dynamics and diversity of Shigella species, the etiologic agents of
RT   bacillary dysentery.";
RL   Nucleic Acids Res. 33:6445-6458(2005).
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; CP000038; AAZ89495.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q3YYB7; -.
DR   SMR; Q3YYB7; -.
DR   EnsemblBacteria; AAZ89495; AAZ89495; SSON_2893.
DR   KEGG; ssn:SSON_2893; -.
DR   HOGENOM; CLU_005281_4_0_6; -.
DR   OMA; LWLWVEK; -.
DR   Proteomes; UP000002529; 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_0000230153"
FT   DOMAIN          155..303
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        80
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   BINDING         27
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   BINDING         129
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   BINDING         329
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   349 AA;  39092 MW;  4534C551EE22244B CRC64;
     MIEFDNLTYL HGKPQGTGLL KANPEDFVVV EDLGFEPDGE GEHILVRILK NGCNTRFVAD
     ALAKFLKIHA REVSFAGQKD KHAVTEQWLC ARVPGKEMPD LSAFQLEGCQ VLEYARHKRK
     LRLGALKGNA FTLVLREVSN RDDVEQRLID ICVKGVPNYF GAQRFGIGGS NLQGAQRWAQ
     TNTPVRDRNK RSFWLSAARS ALFNQIVAER LKKADVNQVV DGDALQLAGR GSWFVATTEE
     LAELQRRVND KELMITAALP GSGEWGTQRE ALAFEKAAVA AETELQALLV REKVEAARRA
     MLLYPQQLSW NWWDDVTVEI RFWLPAGSFA TSVVRELINT TGDYAHIAE