ID   TRUD_METM5              Reviewed;         390 AA.
AC   A4FYL2;
DT   20-MAY-2008, integrated into UniProtKB/Swiss-Prot.
DT   17-APR-2007, sequence version 1.
DT   25-MAY-2022, entry version 78.
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=MmarC5_0990;
OS   Methanococcus maripaludis (strain C5 / ATCC BAA-1333).
OC   Archaea; Euryarchaeota; Methanomada group; Methanococci; Methanococcales;
OC   Methanococcaceae; Methanococcus.
OX   NCBI_TaxID=402880;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=C5 / ATCC BAA-1333;
RG   US DOE Joint Genome Institute;
RA   Copeland A., Lucas S., Lapidus A., Barry K., Glavina del Rio T., Dalin E.,
RA   Tice H., Pitluck S., Chertkov O., Brettin T., Bruce D., Han C.,
RA   Detter J.C., Schmutz J., Larimer F., Land M., Hauser L., Kyrpides N.,
RA   Mikhailova N., Sieprawska-Lupa M., Whitman W.B., Richardson P.;
RT   "Complete sequence of chromosome of Methanococcus maripaludis C5.";
RL   Submitted (MAR-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000609; ABO35296.1; -; Genomic_DNA.
DR   AlphaFoldDB; A4FYL2; -.
DR   SMR; A4FYL2; -.
DR   STRING; 402880.MmarC5_0990; -.
DR   EnsemblBacteria; ABO35296; ABO35296; MmarC5_0990.
DR   KEGG; mmq:MmarC5_0990; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; GFPNYFD; -.
DR   Proteomes; UP000000253; 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; -; 2.
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; 2.
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; tRNA processing.
FT   CHAIN           1..390
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_1000084751"
FT   DOMAIN          166..353
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        93
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   390 AA;  45648 MW;  AA98589A1C61610B CRC64;
     MPININKFIL DMERFDGTLK KYPEDFIVEE ITPEGTVLEV GKEIGFEDVE KWHGSFIHFT
     VEKTNWNTMD ALKQIVRTTK TKRKNFGFAG TKDKFAVTTQ RFGCFGLKKE QLENINIKDI
     VIRDVQKSNK KLRMGDLWGN KFTIKIRGLD LSKKEIKRIS DLKLDYVLNY YGIQRFGLIR
     PITHIVGKFI YERDFESAFY TYCGTPISET GDSLEARQLV DVGEFKKALK LFNRNHDYEK
     RLIQQYLKYK DFKMAFTALP PQLNSMFVNA YQAYLFNEMI NKRFEYGFDA KEGDILEDNT
     PTGTLIGYNT EFSGGIQGEI EKEIVERENL DLKKFKIEDF GNFYGTRRKM ITPIYDFKSS
     FENDIFELSF KLERGNYATI VTREFTGNLS