ID   PUS4_ORYSJ              Reviewed;         448 AA.
AC   Q69K07; A0A0P0XJK3;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   13-SEP-2004, sequence version 1.
DT   03-AUG-2022, entry version 89.
DE   RecName: Full=RNA pseudouridine synthase 4, mitochondrial;
DE            EC=5.4.99.-;
DE   AltName: Full=RNA pseudouridylate synthase 4;
DE   AltName: Full=RNA-uridine isomerase 4;
DE   Flags: Precursor;
GN   OrderedLocusNames=Os09g0103500, LOC_Os09g01620;
GN   ORFNames=OSJNBa0006G10.3, P0414D03.35;
OS   Oryza sativa subsp. japonica (Rice).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC   Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX   NCBI_TaxID=39947;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=16100779; DOI=10.1038/nature03895;
RG   International rice genome sequencing project (IRGSP);
RT   "The map-based sequence of the rice genome.";
RL   Nature 436:793-800(2005).
RN   [2]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=18089549; DOI=10.1093/nar/gkm978;
RG   The rice annotation project (RAP);
RT   "The rice annotation project database (RAP-DB): 2008 update.";
RL   Nucleic Acids Res. 36:D1028-D1033(2008).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Nipponbare;
RX   PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA   Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA   Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA   Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA   Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT   "Improvement of the Oryza sativa Nipponbare reference genome using next
RT   generation sequence and optical map data.";
RL   Rice 6:4-4(2013).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=12869764; DOI=10.1126/science.1081288;
RG   The rice full-length cDNA consortium;
RT   "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT   japonica rice.";
RL   Science 301:376-379(2003).
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=a uridine in RNA = a pseudouridine in RNA;
CC         Xref=Rhea:RHEA:48348, Rhea:RHEA-COMP:12068, Rhea:RHEA-COMP:12069,
CC         ChEBI:CHEBI:65314, ChEBI:CHEBI:65315;
CC   -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC       {ECO:0000305}.
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DR   EMBL; AP005909; BAD34146.1; -; Genomic_DNA.
DR   EMBL; AP006061; BAD36694.1; -; Genomic_DNA.
DR   EMBL; AP008215; BAF24470.1; -; Genomic_DNA.
DR   EMBL; AP014965; BAT06782.1; -; Genomic_DNA.
DR   EMBL; AK065573; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015610651.1; XM_015755165.1.
DR   AlphaFoldDB; Q69K07; -.
DR   STRING; 4530.OS09T0103500-01; -.
DR   PaxDb; Q69K07; -.
DR   PRIDE; Q69K07; -.
DR   EnsemblPlants; Os09t0103500-01; Os09t0103500-01; Os09g0103500.
DR   GeneID; 4346373; -.
DR   Gramene; Os09t0103500-01; Os09t0103500-01; Os09g0103500.
DR   KEGG; osa:4346373; -.
DR   eggNOG; KOG1919; Eukaryota.
DR   HOGENOM; CLU_016902_13_1_1; -.
DR   InParanoid; Q69K07; -.
DR   OMA; KWVRRCC; -.
DR   Proteomes; UP000000763; Chromosome 9.
DR   Proteomes; UP000059680; Chromosome 9.
DR   Genevisible; Q69K07; OS.
DR   GO; GO:0005739; C:mitochondrion; IEA:UniProtKB-SubCell.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IBA:GO_Central.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0000455; P:enzyme-directed rRNA pseudouridine synthesis; IBA:GO_Central.
DR   CDD; cd02869; PseudoU_synth_RluA_like; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR   Pfam; PF00849; PseudoU_synth_2; 1.
DR   SUPFAM; SSF55120; SSF55120; 1.
PE   2: Evidence at transcript level;
KW   Isomerase; Mitochondrion; Reference proteome; RNA-binding; Transit peptide.
FT   TRANSIT         1..69
FT                   /note="Mitochondrion"
FT                   /evidence="ECO:0000255"
FT   CHAIN           70..448
FT                   /note="RNA pseudouridine synthase 4, mitochondrial"
FT                   /id="PRO_0000368025"
FT   DOMAIN          84..170
FT                   /note="S4 RNA-binding"
FT   ACT_SITE        228
FT                   /evidence="ECO:0000250"
FT   CONFLICT        32
FT                   /note="R -> S (in Ref. 4; AK065573)"
FT                   /evidence="ECO:0000305"
FT   CONFLICT        79
FT                   /note="D -> G (in Ref. 4; AK065573)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   448 AA;  49035 MW;  85AD88515EB7283F CRC64;
     MAALLYLRRR AAAAALAGVA PKPQWLATAA RRGALVSGDD GGETGERGKS PWLQLPPFAP
     LDAAAAARAI SRGGGEGGDG EQGATAIKWV RRCCPDLPTS LVQKLFRLRK VKKNVVTAEI
     SSADASAEQH RLRRVSAKDQ LMPGDILFLP VNLKESSVAE KTKKFDNRNE INFLRGLEIY
     KDEAIIVVNK PPGMPVQGGV GIKNSIDVLA SMFEENSSEA PRLVHRLDRD CSGILVLGRN
     QLSTSMLHAI FREKTADALA DGTQHVLQRK YVALVIGTPR HPKGLLSAPL AKILLQDGKS
     ERLTIRASSN AASVQDALTE YRVIESCPQG YTWLELFPRT GRKHQRFLEP QLLGITSMDG
     KRIRSGCLFP CHGQLMRNCS GKGSFPLGLL WVAEASLRSN LSFIYTASKW FFLMSQWLFI
     GCSLQTLILI SQILRSSTLL LHCRCICG