ID   PUS2_ORYSJ              Reviewed;         445 AA.
AC   Q5Z8P2; A0A0P0X198;
DT   14-APR-2009, integrated into UniProtKB/Swiss-Prot.
DT   23-NOV-2004, sequence version 1.
DT   03-AUG-2022, entry version 108.
DE   RecName: Full=RNA pseudouridine synthase 2, chloroplastic;
DE            EC=5.4.99.-;
DE   AltName: Full=RNA pseudouridylate synthase 2;
DE   AltName: Full=RNA-uridine isomerase 2;
DE   Flags: Precursor;
GN   OrderedLocusNames=Os06g0717400, LOC_Os06g50360;
GN   ORFNames=OsJ_22675, P0481E08.45, P0541C02.12;
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].
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   -!- SIMILARITY: Belongs to the pseudouridine synthase RluA family.
CC       {ECO:0000305}.
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DR   EMBL; AP003614; BAD53590.1; -; Genomic_DNA.
DR   EMBL; AP003769; BAD61720.1; -; Genomic_DNA.
DR   EMBL; AP008212; BAF20508.1; -; Genomic_DNA.
DR   EMBL; AP014962; BAS99517.1; -; Genomic_DNA.
DR   EMBL; CM000143; EEE66368.1; -; Genomic_DNA.
DR   EMBL; AK072887; BAG93191.1; -; mRNA.
DR   RefSeq; XP_015642503.1; XM_015787017.1.
DR   AlphaFoldDB; Q5Z8P2; -.
DR   SMR; Q5Z8P2; -.
DR   STRING; 4530.OS06T0717400-01; -.
DR   PaxDb; Q5Z8P2; -.
DR   PRIDE; Q5Z8P2; -.
DR   EnsemblPlants; Os06t0717400-01; Os06t0717400-01; Os06g0717400.
DR   GeneID; 4342081; -.
DR   Gramene; Os06t0717400-01; Os06t0717400-01; Os06g0717400.
DR   KEGG; osa:4342081; -.
DR   eggNOG; KOG1919; Eukaryota.
DR   HOGENOM; CLU_016902_4_3_1; -.
DR   InParanoid; Q5Z8P2; -.
DR   OMA; AHPSPGW; -.
DR   OrthoDB; 1378690at2759; -.
DR   Proteomes; UP000000763; Chromosome 6.
DR   Proteomes; UP000007752; Chromosome 6.
DR   Proteomes; UP000059680; Chromosome 6.
DR   Genevisible; Q5Z8P2; OS.
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   CDD; cd00165; S4; 1.
DR   Gene3D; 3.10.290.10; -; 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   InterPro; IPR036986; S4_RNA-bd_sf.
DR   Pfam; PF00849; PseudoU_synth_2; 1.
DR   Pfam; PF01479; S4; 1.
DR   SMART; SM00363; S4; 1.
DR   SUPFAM; SSF55120; SSF55120; 1.
DR   PROSITE; PS01129; PSI_RLU; 1.
DR   PROSITE; PS50889; S4; 1.
PE   2: Evidence at transcript level;
KW   Chloroplast; Isomerase; Plastid; Reference proteome; RNA-binding;
KW   Transit peptide.
FT   TRANSIT         1..44
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           45..445
FT                   /note="RNA pseudouridine synthase 2, chloroplastic"
FT                   /id="PRO_0000368023"
FT   DOMAIN          72..147
FT                   /note="S4 RNA-binding"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00182"
FT   REGION          47..66
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        235
FT                   /evidence="ECO:0000250"
SQ   SEQUENCE   445 AA;  47839 MW;  C281518D70FB3EBE CRC64;
     MATTAAASPP AIATALSALL RRQRRRSSRC VGASHARCLA ADANAEAVAP SRRGGHGGTR
     LEEAVPAGEG RSRIDAWISA RLGGGGVSRA RIQASIRAGL VVVNGRPVSK VSHMVKGGDI
     VSCTVLELQP LRAEPEDIPL DIVYEDDHLL VVNKPAHMVV HPAPGNANGT LVNAILHHCK
     ISTFTCLARN SIDDECPDSS DDDIDVFDID QFTTGEVSSE VREALVRPGI VHRLDKGTSG
     LLVVAKDEHS HAQLAEQFKL HTIRRVYISL TCGAPNPNSG RIEVPIARDP NNRIRMIATP
     GSGHRYARHA ASRYKVREVF AGGGSALVEW RLETGRTHQI RAHAKYLGIP LLGDETYGGT
     KSMALSLLRP RTPSRYHCDL SNMISKIDRP CLHAALLGFK HPHSGKILEF SCPPPDDFTE
     VLNELHQVTL ASNGNSGGGV ARICD