ID   PUS5_ORYSJ              Reviewed;         397 AA.
AC   Q0DST9; Q10MZ8;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   14-APR-2009, sequence version 2.
DT   03-AUG-2022, entry version 77.
DE   RecName: Full=RNA pseudouridine synthase 5;
DE            EC=5.4.99.-;
DE   AltName: Full=RNA pseudouridylate synthase 5;
DE   AltName: Full=RNA-uridine isomerase 5;
GN   OrderedLocusNames=Os03g0288500, LOC_Os03g17920; ORFNames=OsJ_010020;
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=16109971; DOI=10.1101/gr.3869505;
RG   The rice chromosome 3 sequencing consortium;
RA   Buell C.R., Yuan Q., Ouyang S., Liu J., Zhu W., Wang A., Maiti R., Haas B.,
RA   Wortman J., Pertea M., Jones K.M., Kim M., Overton L., Tsitrin T.,
RA   Fadrosh D., Bera J., Weaver B., Jin S., Johri S., Reardon M., Webb K.,
RA   Hill J., Moffat K., Tallon L., Van Aken S., Lewis M., Utterback T.,
RA   Feldblyum T., Zismann V., Iobst S., Hsiao J., de Vazeille A.R.,
RA   Salzberg S.L., White O., Fraser C.M., Yu Y., Kim H., Rambo T., Currie J.,
RA   Collura K., Kernodle-Thompson S., Wei F., Kudrna K., Ammiraju J.S.S.,
RA   Luo M., Goicoechea J.L., Wing R.A., Henry D., Oates R., Palmer M.,
RA   Pries G., Saski C., Simmons J., Soderlund C., Nelson W., de la Bastide M.,
RA   Spiegel L., Nascimento L., Huang E., Preston R., Zutavern T., Palmer L.,
RA   O'Shaughnessy A., Dike S., McCombie W.R., Minx P., Cordum H., Wilson R.,
RA   Jin W., Lee H.R., Jiang J., Jackson S.;
RT   "Sequence, annotation, and analysis of synteny between rice chromosome 3
RT   and diverged grass species.";
RL   Genome Res. 15:1284-1291(2005).
RN   [2]
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   [3]
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   [4]
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   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Nipponbare;
RX   PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA   Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA   Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA   Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA   Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA   Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA   Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA   Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA   Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA   Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA   Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA   Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA   Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA   Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA   McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT   "The genomes of Oryza sativa: a history of duplications.";
RL   PLoS Biol. 3:266-281(2005).
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   -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=ABF95377.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF11699.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; DP000009; ABF95377.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008209; BAF11699.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014959; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000140; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   RefSeq; XP_015631154.1; XM_015775668.1.
DR   AlphaFoldDB; Q0DST9; -.
DR   SMR; Q0DST9; -.
DR   STRING; 4530.OS03T0288500-01; -.
DR   PRIDE; Q0DST9; -.
DR   GeneID; 4332490; -.
DR   KEGG; osa:4332490; -.
DR   eggNOG; KOG1919; Eukaryota.
DR   InParanoid; Q0DST9; -.
DR   OrthoDB; 1378690at2759; -.
DR   Proteomes; UP000000763; Chromosome 3.
DR   Proteomes; UP000007752; Chromosome 3.
DR   Proteomes; UP000059680; Chromosome 3.
DR   GO; GO:0009982; F:pseudouridine synthase activity; IEA:InterPro.
DR   GO; GO:0003723; F:RNA binding; IEA:UniProtKB-KW.
DR   GO; GO:0001522; P:pseudouridine synthesis; IEA:InterPro.
DR   GO; GO:0006364; P:rRNA processing; IEA:UniProt.
DR   CDD; cd02869; PseudoU_synth_RluA_like; 1.
DR   CDD; cd00165; S4; 1.
DR   InterPro; IPR020103; PsdUridine_synth_cat_dom_sf.
DR   InterPro; IPR006224; PsdUridine_synth_RluC/D_CS.
DR   InterPro; IPR006145; PsdUridine_synth_RsuA/RluA.
DR   InterPro; IPR002942; S4_RNA-bd.
DR   Pfam; PF00849; PseudoU_synth_2; 1.
DR   SUPFAM; SSF55120; SSF55120; 1.
DR   PROSITE; PS01129; PSI_RLU; 1.
PE   2: Evidence at transcript level;
KW   Isomerase; Reference proteome; RNA-binding.
FT   CHAIN           1..397
FT                   /note="RNA pseudouridine synthase 5"
FT                   /id="PRO_0000368026"
FT   DOMAIN          64..114
FT                   /note="S4 RNA-binding"
SQ   SEQUENCE   397 AA;  43696 MW;  27BFFFF6BDE8B63B CRC64;
     MTAAAAAGEI PAEDAPPPGA LYSFGTPWPE FNEGISYIDT FRCADAGATT TLIEFYSTSY
     KSSAPLPGWI KRIRDGQITV DGEVATDPDM ILREGSKLVY HRLPWQEPFA PHLLDVLYED
     DDMIALNKPS GLQVLPKGLF QQRTVLAQLQ LKDWKMPSSF CSKRKDAQSH PVPVHRLGRG
     TSGLLLCAKT KLAKAQLAAY FAEGATNAGK SRDETDICKA RKISKFYRAL VTGILENDEV
     MITQPIGLVR YPGVAEGLYA ACSSGKPAMS KVRVLERLKI HNHTLIQVEI HSGRPHQIRI
     HLAYIGHPLV DDPLYGIGGQ PKFDEPEPTS TADSFAYDGG YERPLQPVPG DCGYHLHAHW
     LVLCHPTTNE MIKITAPLPH ILQTREEQQD TAKLLGG