ID   TRUD_NATPD              Reviewed;         435 AA.
AC   Q3IMF3;
DT   04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT   08-NOV-2005, sequence version 1.
DT   25-MAY-2022, entry version 90.
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=NP_5228A;
OS   Natronomonas pharaonis (strain ATCC 35678 / DSM 2160 / CIP 103997 / JCM
OS   8858 / NBRC 14720 / NCIMB 2260 / Gabara) (Halobacterium pharaonis).
OC   Archaea; Euryarchaeota; Stenosarchaea group; Halobacteria; Halobacteriales;
OC   Haloarculaceae; Natronomonas.
OX   NCBI_TaxID=348780;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=ATCC 35678 / DSM 2160 / CIP 103997 / JCM 8858 / NBRC 14720 / NCIMB
RC   2260 / Gabara;
RX   PubMed=16169924; DOI=10.1101/gr.3952905;
RA   Falb M., Pfeiffer F., Palm P., Rodewald K., Hickmann V., Tittor J.,
RA   Oesterhelt D.;
RT   "Living with two extremes: conclusions from the genome sequence of
RT   Natronomonas pharaonis.";
RL   Genome Res. 15:1336-1343(2005).
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; CR936257; CAI50705.1; -; Genomic_DNA.
DR   RefSeq; WP_011324315.1; NC_007426.1.
DR   AlphaFoldDB; Q3IMF3; -.
DR   SMR; Q3IMF3; -.
DR   STRING; 348780.NP_5228A; -.
DR   EnsemblBacteria; CAI50705; CAI50705; NP_5228A.
DR   GeneID; 3702304; -.
DR   KEGG; nph:NP_5228A; -.
DR   eggNOG; arCOG04252; Archaea.
DR   HOGENOM; CLU_005281_4_1_2; -.
DR   OMA; GFPNYFD; -.
DR   OrthoDB; 92795at2157; -.
DR   Proteomes; UP000002698; 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..435
FT                   /note="Probable tRNA pseudouridine synthase D"
FT                   /id="PRO_0000230160"
FT   DOMAIN          170..396
FT                   /note="TRUD"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
FT   ACT_SITE        95
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_01082"
SQ   SEQUENCE   435 AA;  47903 MW;  3A90970EE4F57952 CRC64;
     MRDSHPVEQT VGIEYYVTET DGTGGRLRDR PADFRVRERE AFGADCRPLD ADPGSYPHLV
     FRATLREWDT NDFASAVSNA LGVSRERVSW AGTKDKHAVT TQLFSVRHDD AALPDLDGAD
     IEPIGRAGRP VLFGDLAGNE FELVIRDPDR PEHAEATAAE LCDFGGGEAG VPNYFGTQRF
     GSRRPITHRV GLDVLDGDWE AAAVRYVCES SEREPERTQE VREGIDADRD WAAAGERLPG
     SLRFERAIAN RLAEGAESPD DYRAALEELP SNLQRMFVNA AQSYVFNRIL SERLRRGLPF
     DEPVVGDVVC FSDSDGNPDP DRTQTVTESR LETVRRHCER GRAFVTAPLV GTETVFGDGE
     PAEITREVLA DVDVSPTDFE LPGEFGSSGT RRAVLVTTDL TVEQEPLTLS FSLPKGSYAT
     VVAREFLKAD PEALS