ID   PUS6_ORYSJ              Reviewed;         477 AA.
AC   A3BN26; Q7EZZ2;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   20-MAR-2007, sequence version 1.
DT   03-AUG-2022, entry version 80.
DE   RecName: Full=RNA pseudouridine synthase 6, chloroplastic;
DE            EC=5.4.99.-;
DE   AltName: Full=RNA pseudouridylate synthase 6;
DE   AltName: Full=RNA-uridine isomerase 6;
DE   Flags: Precursor;
GN   OrderedLocusNames=Os07g0660400, LOC_Os07g46600;
GN   ORFNames=OsJ_024448, P0496C02.118;
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 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).
RN   [5]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
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: Plastid, chloroplast {ECO:0000305}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=A3BN26-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=A3BN26-2; Sequence=VSP_036778;
CC   -!- MISCELLANEOUS: [Isoform 2]: May be due to a competing acceptor splice
CC       site. {ECO:0000305}.
CC   -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC       {ECO:0000305}.
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DR   EMBL; AP004378; BAC83571.1; -; Genomic_DNA.
DR   EMBL; AP008213; BAF22445.1; -; Genomic_DNA.
DR   EMBL; AP014963; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR   EMBL; CM000144; EAZ40965.1; -; Genomic_DNA.
DR   EMBL; AK065105; -; NOT_ANNOTATED_CDS; mRNA.
DR   RefSeq; XP_015647803.1; XM_015792317.1. [A3BN26-1]
DR   AlphaFoldDB; A3BN26; -.
DR   STRING; 4530.OS07T0660400-01; -.
DR   PaxDb; A3BN26; -.
DR   PRIDE; A3BN26; -.
DR   GeneID; 112936104; -.
DR   KEGG; osa:4344176; -.
DR   eggNOG; KOG1919; Eukaryota.
DR   InParanoid; A3BN26; -.
DR   Proteomes; UP000000763; Chromosome 7.
DR   Proteomes; UP000007752; Chromosome 7.
DR   Proteomes; UP000059680; Chromosome 7.
DR   GO; GO:0009507; C:chloroplast; 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   Alternative splicing; Chloroplast; Isomerase; Plastid; Reference proteome;
KW   RNA-binding; Transit peptide.
FT   TRANSIT         1..52
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           53..477
FT                   /note="RNA pseudouridine synthase 6, chloroplastic"
FT                   /id="PRO_0000368027"
FT   DOMAIN          98..205
FT                   /note="S4 RNA-binding"
FT   ACT_SITE        258
FT                   /evidence="ECO:0000250"
FT   VAR_SEQ         2..117
FT                   /note="PKAAASLASLLPQLWHRPVQPPPFLHRALSSSSPLLRRHRAALHSPAAPLSA
FT                   AAVSTSAATVEAPATAAYPVYGRLLPCPLQDDPPRIEHLVAREDEVAVDFISRSLTLPP
FT                   LYVAD -> AGSCLALCKMTLQGSSTSSRGKTRSPSISSPGHSPSLHY (in
FT                   isoform 2)"
FT                   /evidence="ECO:0000303|PubMed:12869764"
FT                   /id="VSP_036778"
FT   CONFLICT        279
FT                   /note="G -> R (in Ref. 5; AK065105)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   477 AA;  52881 MW;  8A61DFF902EF161F CRC64;
     MPKAAASLAS LLPQLWHRPV QPPPFLHRAL SSSSPLLRRH RAALHSPAAP LSAAAVSTSA
     ATVEAPATAA YPVYGRLLPC PLQDDPPRIE HLVAREDEVA VDFISRSLTL PPLYVADLIK
     FGAVYYALVA PQPPPHAAPE HVRIFREVTE PSVLCRRKSI KGKTVREAQK TFRVTDPNQR
     LEAGTYLRVH VHPKRFPRCY EIDWKSRVIA VTDNYVVLDK PAATSVGGAT DNIEESCVVF
     TSRALGLETP LMTTHQIDNC SEGCVVLSKT KEFCSVFHGM IREKQVNKRY LALTTAPVST
     GIITHYMRPI NRAPRLVSED HIKGWHVCQM EILDCKKVPW PSSLIRKVHK VDNCGWPQQE
     AAYECKINLL TGKTHQIRAQ LAAIGTPIVG DSAYMTAAMA AIVNPSINPF GRWGQNYDSE
     DEKAAAVEAW ISCHGKEPKS VIGLQASEIS WDYEGEHHSY KAGVPWWRQD AVESDLI