ID   TRUD2_METJA             Reviewed;         422 AA.
AC   Q58759;
DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   26-SEP-2003, sequence version 2.
DT   25-MAY-2022, entry version 103.
DE   RecName: Full=Probable tRNA pseudouridine synthase D 2 {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 2 {ECO:0000255|HAMAP-Rule:MF_01082};
DE   AltName: Full=tRNA-uridine isomerase D 2 {ECO:0000255|HAMAP-Rule:MF_01082};
GN   Name=truD2 {ECO:0000255|HAMAP-Rule:MF_01082}; OrderedLocusNames=MJ1364;
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=AAB99372.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR   EMBL; L77117; AAB99372.1; ALT_INIT; Genomic_DNA.
DR   PIR; C64470; C64470.
DR   AlphaFoldDB; Q58759; -.
DR   SMR; Q58759; -.
DR   STRING; 243232.MJ_1364; -.
DR   EnsemblBacteria; AAB99372; AAB99372; MJ_1364.
DR   KEGG; mja:MJ_1364; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   InParanoid; Q58759; -.
DR   OMA; IGYCGLK; -.
DR   PhylomeDB; Q58759; -.
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; -; 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; 1.
DR   Pfam; PF01142; TruD; 1.
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..422
FT                   /note="Probable tRNA pseudouridine synthase D 2"
FT                   /id="PRO_0000152541"
FT   DOMAIN          160..371
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        89
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   422 AA;  50180 MW;  BDADF2BBA901F6E4 CRC64;
     MKNISTKESF FKFKFNNRSL YCWGAFMKLR MKPEDFIVEE IIDFNKIAGD RCYLYKLTKR
     NIESLKAFSY IAKKFKIPLK DIGYCGLKDR HALTTQYISI PKKYGKLSLD EPNLKLELIG
     ESKFLLLGDL EGNRFTITVR GLKKEDIPKI KENLKYLEFG APNYFDSQRF GSVFDKKFIA
     KEVIKGNYEE AVKILLTKYK KSEKKLIKDL KRFIDKNWGD WDKIWEYIKE NNIKSRLYVN
     MVKELKKSND YKKALSYVDD RLKKIFVAAY QSYLWNECVK ELLRKYVPEE DRVYYEYECG
     TLMFYKKMDE EVFNILKDKK FPTIAPDIEY SGEEKEIIEE ILKREGLTME ELNNIGELGK
     FIYSERKILS IPKNLKIGEF EEDELNKGKY KITLSYELEK GSYATIIIKR AFLGVKTKKR
     KR