ID   TRUD_SHEON              Reviewed;         370 AA.
AC   Q8EBR4;
DT   26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-MAR-2003, sequence version 1.
DT   03-AUG-2022, entry version 102.
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=SO_3436;
OS   Shewanella oneidensis (strain MR-1).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC   Shewanellaceae; Shewanella.
OX   NCBI_TaxID=211586;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=MR-1;
RX   PubMed=12368813; DOI=10.1038/nbt749;
RA   Heidelberg J.F., Paulsen I.T., Nelson K.E., Gaidos E.J., Nelson W.C.,
RA   Read T.D., Eisen J.A., Seshadri R., Ward N.L., Methe B.A., Clayton R.A.,
RA   Meyer T., Tsapin A., Scott J., Beanan M.J., Brinkac L.M., Daugherty S.C.,
RA   DeBoy R.T., Dodson R.J., Durkin A.S., Haft D.H., Kolonay J.F., Madupu R.,
RA   Peterson J.D., Umayam L.A., White O., Wolf A.M., Vamathevan J.J.,
RA   Weidman J.F., Impraim M., Lee K., Berry K.J., Lee C., Mueller J.,
RA   Khouri H.M., Gill J., Utterback T.R., McDonald L.A., Feldblyum T.V.,
RA   Smith H.O., Venter J.C., Nealson K.H., Fraser C.M.;
RT   "Genome sequence of the dissimilatory metal ion-reducing bacterium
RT   Shewanella oneidensis.";
RL   Nat. Biotechnol. 20:1118-1123(2002).
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; AE014299; AAN56433.1; -; Genomic_DNA.
DR   RefSeq; NP_718989.1; NC_004347.2.
DR   RefSeq; WP_011073292.1; NZ_CP053946.1.
DR   AlphaFoldDB; Q8EBR4; -.
DR   SMR; Q8EBR4; -.
DR   STRING; 211586.SO_3436; -.
DR   PaxDb; Q8EBR4; -.
DR   KEGG; son:SO_3436; -.
DR   PATRIC; fig|211586.12.peg.3331; -.
DR   eggNOG; COG0585; Bacteria.
DR   HOGENOM; CLU_005281_4_0_6; -.
DR   OMA; LWLWVEK; -.
DR   OrthoDB; 1490777at2; -.
DR   PhylomeDB; Q8EBR4; -.
DR   BioCyc; SONE211586:G1GMP-3207-MON; -.
DR   Proteomes; UP000008186; Chromosome.
DR   GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:InterPro.
DR   GO; GO:0106029; F:tRNA pseudouridine synthase activity; IEA:UniProtKB-EC.
DR   GO; GO:0001522; P:pseudouridine synthesis; IBA:GO_Central.
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   PROSITE; PS50984; TRUD; 1.
DR   PROSITE; PS01268; UPF0024; 1.
PE   3: Inferred from homology;
KW   Isomerase; Reference proteome; tRNA processing.
FT   CHAIN           1..370
FT                   /note="tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152521"
FT   DOMAIN          152..297
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   370 AA;  41298 MW;  A9797D03EFB9C9C6 CRC64;
     MSELHYLYGK PTGTADLRTV NSDFIVKEIL PFSPSGEGEH HLVHIRKDGL NTVQVAEMLA
     KFAKVHPKEV TYAGQKDKNA ITEQWFGIRI PGKETPAWIE LNSDRLTVLS SSRHSKKLRI
     GALLGNRFIL TLRNVTNVED IISRIEKVSQ IGVPNYFGEQ RFGHDGKNLV LGRQMLAGKK
     VKDRNKRSMY LSAVRSHLFN TVVSYRLTHY GTRPLAGDCV MLAGSKSFFV TPEWDLVVLK
     RLIEKDIQLS APLWGRGKML PQGEAAEVET QAMADLTEDC YGLEHAGLEQ ERRPLLLEPQ
     GLKHEQTSDG LVLEFILPAG CFATSLLREL VDYQDVKELQ WQTTLTAETN VVTESNTAAA
     NVSDNGESAS