ID   TRUD1_METMP             Reviewed;         389 AA.
AC   Q6M1A3;
DT   26-APR-2005, integrated into UniProtKB/Swiss-Prot.
DT   05-JUL-2004, sequence version 1.
DT   03-AUG-2022, entry version 86.
DE   RecName: Full=Probable tRNA pseudouridine synthase D 1;
DE            EC=5.4.99.27;
DE   AltName: Full=tRNA pseudouridine(13) synthase;
DE   AltName: Full=tRNA pseudouridylate synthase D 1;
DE   AltName: Full=tRNA-uridine isomerase D 1;
GN   Name=truD1; OrderedLocusNames=MMP0014;
OS   Methanococcus maripaludis (strain S2 / LL).
OC   Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC   Methanococcaceae; Methanococcus.
OX   NCBI_TaxID=267377;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=S2 / LL;
RX   PubMed=15466049; DOI=10.1128/jb.186.20.6956-6969.2004;
RA   Hendrickson E.L., Kaul R., Zhou Y., Bovee D., Chapman P., Chung J.,
RA   Conway de Macario E., Dodsworth J.A., Gillett W., Graham D.E., Hackett M.,
RA   Haydock A.K., Kang A., Land M.L., Levy R., Lie T.J., Major T.A.,
RA   Moore B.C., Porat I., Palmeiri A., Rouse G., Saenphimmachak C., Soell D.,
RA   Van Dien S., Wang T., Whitman W.B., Xia Q., Zhang Y., Larimer F.W.,
RA   Olson M.V., Leigh J.A.;
RT   "Complete genome sequence of the genetically tractable hydrogenotrophic
RT   methanogen Methanococcus maripaludis.";
RL   J. Bacteriol. 186:6956-6969(2004).
CC   -!- FUNCTION: Could be responsible for synthesis of pseudouridine from
CC       uracil-13 in transfer RNAs. {ECO:0000250}.
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   -!- SIMILARITY: Belongs to the pseudouridine synthase TruD family.
CC       {ECO:0000305}.
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DR   EMBL; BX950229; CAF29570.1; -; Genomic_DNA.
DR   RefSeq; WP_011169958.1; NC_005791.1.
DR   AlphaFoldDB; Q6M1A3; -.
DR   SMR; Q6M1A3; -.
DR   STRING; 267377.MMP0014; -.
DR   PRIDE; Q6M1A3; -.
DR   EnsemblBacteria; CAF29570; CAF29570; MMP0014.
DR   GeneID; 2762446; -.
DR   KEGG; mmp:MMP0014; -.
DR   PATRIC; fig|267377.15.peg.14; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; IGYCGLK; -.
DR   OrthoDB; 92795at2157; -.
DR   BioCyc; MMAR267377:MMP_RS00100-MON; -.
DR   Proteomes; UP000000590; 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:0001522; P:pseudouridine synthesis; IEA:InterPro.
DR   GO; GO:0008033; P:tRNA processing; IEA:UniProtKB-KW.
DR   Gene3D; 3.30.2350.20; -; 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..389
FT                   /note="Probable tRNA pseudouridine synthase D 1"
FT                   /id="PRO_0000152544"
FT   DOMAIN          135..345
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00342"
FT   ACT_SITE        63
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   389 AA;  46201 MW;  15F89137BFB03189 CRC64;
     MKFRQKHEDF IVNEILEYEL NDYGNYFLYK LQKNGIENLK AISYLSKNFE VPTKEIGYCG
     LKDRHAITTQ YVSIPKEYGK LSLDEDNLKL EYVGTIEKPL KIGRLYGNRF EIIARAVDKD
     EFLKIADNIR NLSSGAPNYY DDQRFGSVFN GKFIAKEILK GNYEEVVKIL LTSYTKSEKK
     QLKDLKRFIA KNWGNWDECL EYIDKKQIRS KMFRNMVKSL TYENDFKKAF KYVDNRLKEL
     FISAYQSYLW NECLKEFLKE VIPKENRIYV DYSCGTFLFY ENIEEELFDK LKEMDFPTIV
     SDVEYTDPEK RIIKAILKKE RIKISDFEKL DFGKLKYTKR PIISIPEDVN TGKFKSDELN
     SKKYKIDLEF SLKKGSYATI ILKRVFNIL