ID   TRUD1_METJA             Reviewed;         392 AA.
AC   Q58008;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   26-SEP-2003, sequence version 2.
DT   25-MAY-2022, entry version 115.
DE   RecName: Full=Probable tRNA pseudouridine synthase D 1 {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 1 {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA-uridine isomerase D 1 {ECO:0000255|HAMAP-Rule:MF_01082};
GN   Name=truD1 {ECO:0000255|HAMAP-Rule:MF_01082}; OrderedLocusNames=MJ0588;
OS   Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM
OS   10045 / NBRC 100440) (Methanococcus jannaschii).
OC   Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC   Methanocaldococcaceae; Methanocaldococcus.
OX   NCBI_TaxID=243232;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440;
RX   PubMed=8688087; DOI=10.1126/science.273.5278.1058;
RA   Bult C.J., White O., Olsen G.J., Zhou L., Fleischmann R.D., Sutton G.G.,
RA   Blake J.A., FitzGerald L.M., Clayton R.A., Gocayne J.D., Kerlavage A.R.,
RA   Dougherty B.A., Tomb J.-F., Adams M.D., Reich C.I., Overbeek R.,
RA   Kirkness E.F., Weinstock K.G., Merrick J.M., Glodek A., Scott J.L.,
RA   Geoghagen N.S.M., Weidman J.F., Fuhrmann J.L., Nguyen D., Utterback T.R.,
RA   Kelley J.M., Peterson J.D., Sadow P.W., Hanna M.C., Cotton M.D.,
RA   Roberts K.M., Hurst M.A., Kaine B.P., Borodovsky M., Klenk H.-P.,
RA   Fraser C.M., Smith H.O., Woese C.R., Venter J.C.;
RT   "Complete genome sequence of the methanogenic archaeon, Methanococcus
RT   jannaschii.";
RL   Science 273:1058-1073(1996).
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}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAB98579.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; L77117; AAB98579.1; ALT_INIT; Genomic_DNA.
DR   PIR; D64373; D64373.
DR   AlphaFoldDB; Q58008; -.
DR   SMR; Q58008; -.
DR   STRING; 243232.MJ_0588; -.
DR   EnsemblBacteria; AAB98579; AAB98579; MJ_0588.
DR   KEGG; mja:MJ_0588; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   InParanoid; Q58008; -.
DR   OMA; GFPNYFD; -.
DR   PhylomeDB; Q58008; -.
DR   Proteomes; UP000000805; Chromosome.
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; 3.30.2350.20; -; 3.
DR   HAMAP; MF_01082; TruD; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR001656; PsdUridine_synth_TruD.
DR   InterPro; IPR011760; PsdUridine_synth_TruD_insert.
DR   InterPro; IPR042214; TruD_catalytic.
DR   PANTHER; PTHR13326; PTHR13326; 1.
DR   Pfam; PF01142; TruD; 2.
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..392
FT                   /note="Probable tRNA pseudouridine synthase D 1"
FT                   /id="PRO_0000152540"
FT   DOMAIN          167..354
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        92
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   392 AA;  46320 MW;  DC00CC533E6E065C CRC64;
     MPLNMNKYLT DAYTGGIIKK YPEDFIVEEI TPEGIILEVG KSIEFKDEEN WKGNYIHFTL
     EKRNWTTLDA IREIANRVGK QRKHFGFAGN KDKYAVTTQR VGCFNVKLED LMKVKIKGII
     LRDFQKTNRK IRLGDLWGNR FTIRVREPEL KGKELEEALN KLCKLKYFLN YYGVQRFGTT
     RPITHIVGRF IIERDWEGAF HAYCGTPLPY DDKKSKLARE LVDEENFKEA YKKFPKAFFY
     ERRMIKAYIE TGSYQKAFMI LPPYLRCMFI NAYQSYLFNE IINRRFEYGF EPMEGDILID
     NVPSGALFGY KTRFASGIQG EIEREIYERE NLSPEDFKIG EFGSFIGDRR AMIGKIYNMK
     YWIEDDSYVL QFCLKKGNYA TSVLREFIEK KD