ID   TRUD_ARCFU              Reviewed;         411 AA.
AC   O28596;
DT   26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-JAN-1998, sequence version 1.
DT   25-MAY-2022, entry version 110.
DE   RecName: Full=Probable 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=AF_1677;
OS   Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC
OS   100126 / VC-16).
OC   Archaea; Euryarchaeota; Archaeoglobi; Archaeoglobales; Archaeoglobaceae;
OC   Archaeoglobus.
OX   NCBI_TaxID=224325;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16;
RX   PubMed=9389475; DOI=10.1038/37052;
RA   Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A.,
RA   Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L.,
RA   Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D.,
RA   Quackenbush J., Lee N.H., Sutton G.G., Gill S.R., Kirkness E.F.,
RA   Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N.,
RA   Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R.,
RA   Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D.,
RA   Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P.,
RA   Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M.,
RA   Smith H.O., Woese C.R., Venter J.C.;
RT   "The complete genome sequence of the hyperthermophilic, sulphate-reducing
RT   archaeon Archaeoglobus fulgidus.";
RL   Nature 390:364-370(1997).
CC   -!- FUNCTION: Could be responsible for synthesis of pseudouridine from
CC       uracil-13 in 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; AE000782; AAB89568.1; -; Genomic_DNA.
DR   PIR; D69459; D69459.
DR   RefSeq; WP_010879173.1; NC_000917.1.
DR   AlphaFoldDB; O28596; -.
DR   SMR; O28596; -.
DR   STRING; 224325.AF_1677; -.
DR   EnsemblBacteria; AAB89568; AAB89568; AF_1677.
DR   GeneID; 24795420; -.
DR   KEGG; afu:AF_1677; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   PhylomeDB; O28596; -.
DR   Proteomes; UP000002199; 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; 3.30.2350.20; -; 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   PANTHER; PTHR13326; PTHR13326; 2.
DR   Pfam; PF01142; TruD; 1.
DR   PIRSF; PIRSF037016; Pseudouridin_synth_euk_prd; 1.
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..411
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152536"
FT   DOMAIN          154..375
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   411 AA;  47716 MW;  109B5250D969922E CRC64;
     MEEKVGIECY ITSTPGMGGE IKAEPEDFYV EEIAEFNLSD EGDFLIIRVE KKNWDTLNFA
     RVLSNALGIS QKRISFAGTK DKRALTVQYF SIYGVKKEEI ERVNLKDAKI EVIGYARRAI
     QLGDLLGNFF RIRVYGCRDG EIFQETRNEL MEKGTPNFFG LQRFGSIRFI THEVGKLILQ
     NNYEEAFWVY VAKPFEGENE EVRKIREILW ETRDAKLGLR ELPKYLRYER NLLQKLREGK
     SEEEALLSLP KNLKMMFVHA YQSYIFNRLL SERIRQFGSL KTLEEGDFAC YLTFKTRPTF
     SDCSEVEVNE ARVRFLVKER VASLALPLVG YDTKLKGWSR IALDFLSEDN LDLSSFKTKH
     KEFSSSGSYR PADTLIEHTG LSFTDSTFSF YLPRGCYATV FLREFLKTEL S