ID   TRUD_METBU              Reviewed;         439 AA.
AC   Q12WH6;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   22-AUG-2006, sequence version 1.
DT   25-MAY-2022, entry version 88.
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=Mbur_1281;
OS   Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / OCM 468 /
OS   ACE-M).
OC   Archaea; Euryarchaeota; Stenosarchaea group; Methanomicrobia;
OC   Methanosarcinales; Methanosarcinaceae; Methanococcoides.
OX   NCBI_TaxID=259564;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=DSM 6242 / NBRC 107633 / OCM 468 / ACE-M;
RX   PubMed=19404327; DOI=10.1038/ismej.2009.45;
RA   Allen M.A., Lauro F.M., Williams T.J., Burg D., Siddiqui K.S.,
RA   De Francisci D., Chong K.W., Pilak O., Chew H.H., De Maere M.Z., Ting L.,
RA   Katrib M., Ng C., Sowers K.R., Galperin M.Y., Anderson I.J., Ivanova N.,
RA   Dalin E., Martinez M., Lapidus A., Hauser L., Land M., Thomas T.,
RA   Cavicchioli R.;
RT   "The genome sequence of the psychrophilic archaeon, Methanococcoides
RT   burtonii: the role of genome evolution in cold adaptation.";
RL   ISME J. 3:1012-1035(2009).
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; CP000300; ABE52200.1; -; Genomic_DNA.
DR   RefSeq; WP_011499345.1; NC_007955.1.
DR   AlphaFoldDB; Q12WH6; -.
DR   SMR; Q12WH6; -.
DR   STRING; 259564.Mbur_1281; -.
DR   EnsemblBacteria; ABE52200; ABE52200; Mbur_1281.
DR   GeneID; 3998305; -.
DR   KEGG; mbu:Mbur_1281; -.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   Proteomes; UP000001979; 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; 1.
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..439
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_1000084750"
FT   DOMAIN          166..391
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        87
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   439 AA;  49945 MW;  61F501948EEC417C CRC64;
     MNNVPNVEKQ IGIDLYTTKT PGIGGKLRQQ TEDFGVIEIT NREEGTEGKY LILELTKRNW
     ETHHLIRDLT RILRISQKRV GFAGTKDKRA VTTQKISIYD MEEEALQNVH LKDTELKILG
     RSNKSLELGD LTGNEFIITV RDIDLDEKEL ESRLSQTTAS IKEQGGVPNF FGIQRFGALR
     PITHVVGESI VRNDIEKAAM AYIAASYPDE PEDTQEVRNR VFETKDYIEG LKGYPLQLRY
     ERAMMHHLVS KPEDYAGSFE TLPANIRKMF VHAYQSYIYN TIICSRIKKG LPLNRAVVGD
     IVCFKNKAGL PDKSRNERVT EDNIDGMNNL VKRNRAFVTA PLVGYSSELA SGVPGEIERE
     VIEELNVPIE GFKVPSMEEL SSKGLRREIL LSTDPKYFIE EDELNEGKYR VTLDFSLPKG
     SYATTILREY MKVEPLKMS