ID   TRUD_METAC              Reviewed;         441 AA.
AC   Q8TKX2;
DT   26-SEP-2003, integrated into UniProtKB/Swiss-Prot.
DT   01-JUN-2002, sequence version 1.
DT   27-MAR-2024, entry version 111.
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};
GN   OrderedLocusNames=MA_3271;
OS   Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 / JCM 12185 /
OS   C2A).
OC   Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC   Methanosarcinales; Methanosarcinaceae; Methanosarcina.
OX   NCBI_TaxID=188937;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 35395 / DSM 2834 / JCM 12185 / C2A;
RX   PubMed=11932238; DOI=10.1101/gr.223902;
RA   Galagan J.E., Nusbaum C., Roy A., Endrizzi M.G., Macdonald P., FitzHugh W.,
RA   Calvo S., Engels R., Smirnov S., Atnoor D., Brown A., Allen N., Naylor J.,
RA   Stange-Thomann N., DeArellano K., Johnson R., Linton L., McEwan P.,
RA   McKernan K., Talamas J., Tirrell A., Ye W., Zimmer A., Barber R.D.,
RA   Cann I., Graham D.E., Grahame D.A., Guss A.M., Hedderich R.,
RA   Ingram-Smith C., Kuettner H.C., Krzycki J.A., Leigh J.A., Li W., Liu J.,
RA   Mukhopadhyay B., Reeve J.N., Smith K., Springer T.A., Umayam L.A.,
RA   White O., White R.H., de Macario E.C., Ferry J.G., Jarrell K.F., Jing H.,
RA   Macario A.J.L., Paulsen I.T., Pritchett M., Sowers K.R., Swanson R.V.,
RA   Zinder S.H., Lander E., Metcalf W.W., Birren B.;
RT   "The genome of Methanosarcina acetivorans reveals extensive metabolic and
RT   physiological diversity.";
RL   Genome Res. 12:532-542(2002).
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; AE010299; AAM06642.1; -; Genomic_DNA.
DR   AlphaFoldDB; Q8TKX2; -.
DR   SMR; Q8TKX2; -.
DR   STRING; 188937.MA_3271; -.
DR   EnsemblBacteria; AAM06642; AAM06642; MA_3271.
DR   KEGG; mac:MA_3271; -.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   InParanoid; Q8TKX2; -.
DR   PhylomeDB; Q8TKX2; -.
DR   Proteomes; UP000002487; 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   CDD; cd02577; PSTD1; 1.
DR   Gene3D; 1.10.1510.30; -; 1.
DR   Gene3D; 3.30.70.3160; -; 1.
DR   Gene3D; 3.30.2350.20; TruD, catalytic domain; 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   NCBIfam; TIGR00094; tRNA_TruD_broad; 1.
DR   PANTHER; PTHR13326:SF21; PSEUDOURIDYLATE SYNTHASE PUS7L; 1.
DR   PANTHER; PTHR13326; TRNA PSEUDOURIDINE SYNTHASE D; 1.
DR   Pfam; PF01142; TruD; 1.
DR   PIRSF; PIRSF037016; Pseudouridin_synth_euk_prd; 1.
DR   SUPFAM; SSF55120; Pseudouridine synthase; 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..441
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_0000152539"
FT   DOMAIN          168..393
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   441 AA;  50058 MW;  A3A401EA4D900365 CRC64;
     MQPMEVPEIE KQIGINLYST NTEGLGGRLR QEVEDFIVKE ITNREEGKDG RYLVLELTKR
     DWDTHHFTRT LAKILQISQK RISVAGTKDK RALTTQKISI FDIDALEIEK IHLKDVELKV
     LGRSRKSVEL GDLWGNEFII TIRDISSSPE ETRTILEKTN SKVLTQGGVP NFFGVQRFGS
     VRSVTHLVGK AIVEGNFEKA AMLYIAEPFP EEPEETKAAR QFVKETRDFK EGLKTYPLRL
     GHERAMMNHL ISNPEDYSGA FSVLPKNLYR MFVHAYQSYI YNMILCRRIE SGISLNRAVE
     GDIVCFRNEA GLPDSSKTEK VTSETVNAMN RLIKHGRAFI TAPLPGFNTE FASGVPGEIE
     SKILKELRVS LEGFNVEEFP EMSSKGTRRE VLLQVEPKFE VGEDELNPGK SKTVLEFMLP
     KGSYATTVLR EYMKVDPLQM S
//