ID   SPP_ORYSJ               Reviewed;        1246 AA.
AC   Q69TY5; A0A0P0WZ97; B7ECD6; B9FQ02; Q0DAU7;
DT   16-MAR-2016, integrated into UniProtKB/Swiss-Prot.
DT   16-MAR-2016, sequence version 2.
DT   03-AUG-2022, entry version 89.
DE   RecName: Full=Stromal processing peptidase, chloroplastic {ECO:0000305};
DE            EC=3.4.24.- {ECO:0000250|UniProtKB:Q40983};
DE   Flags: Precursor;
GN   Name=SPP {ECO:0000305};
GN   OrderedLocusNames=Os06g0625400 {ECO:0000312|EMBL:BAF20026.1,
GN   ECO:0000312|EMBL:BAS98693.1}, LOC_Os06g41990 {ECO:0000305};
GN   ORFNames=OSJNBa0029G06.38-1 {ECO:0000312|EMBL:BAD35692.1},
GN   OSJNBa0072A21.7-1 {ECO:0000312|EMBL:BAD37737.1};
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   -!- FUNCTION: Cleaves presequences (transit peptides) from chloroplastic
CC       protein precursors. Initially recognizes a precursor by binding to the
CC       C-terminus of its transit peptide and then removes the transit peptide
CC       in a single endoproteolytic step. In a next step, pursues the cleavage
CC       of transit peptide to a subfragment form.
CC       {ECO:0000250|UniProtKB:Q40983}.
CC   -!- COFACTOR:
CC       Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC         Evidence={ECO:0000250|UniProtKB:Q40983};
CC       Note=Binds 1 zinc ion per subunit. {ECO:0000250|UniProtKB:Q40983};
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast stroma
CC       {ECO:0000250|UniProtKB:Q40983}.
CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1;
CC         IsoId=Q69TY5-1; Sequence=Displayed;
CC       Name=2;
CC         IsoId=Q69TY5-2; Sequence=VSP_058158;
CC   -!- SIMILARITY: Belongs to the peptidase M16 family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAD35692.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD37737.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF20026.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAS98693.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAS98694.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=EEE66044.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC   ---------------------------------------------------------------------------
CC   Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC   Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC   ---------------------------------------------------------------------------
DR   EMBL; AP004680; BAD35692.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP004737; BAD37737.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008212; BAF20026.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014962; BAS98693.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014962; BAS98694.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CM000143; EEE66044.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AK066566; BAG90033.1; -; mRNA.
DR   RefSeq; XP_015643311.1; XM_015787825.1. [Q69TY5-1]
DR   AlphaFoldDB; Q69TY5; -.
DR   SMR; Q69TY5; -.
DR   STRING; 4530.OS06T0625400-01; -.
DR   MEROPS; M16.004; -.
DR   PaxDb; Q69TY5; -.
DR   PRIDE; Q69TY5; -.
DR   GeneID; 4341569; -.
DR   KEGG; osa:4341569; -.
DR   eggNOG; KOG0959; Eukaryota.
DR   InParanoid; Q69TY5; -.
DR   OrthoDB; 148438at2759; -.
DR   Proteomes; UP000000763; Chromosome 6.
DR   Proteomes; UP000007752; Chromosome 6.
DR   Proteomes; UP000059680; Chromosome 6.
DR   GO; GO:0009570; C:chloroplast stroma; IEA:UniProtKB-SubCell.
DR   GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR   GO; GO:0008237; F:metallopeptidase activity; IEA:UniProtKB-KW.
DR   GO; GO:0006508; P:proteolysis; IEA:UniProtKB-KW.
DR   InterPro; IPR011249; Metalloenz_LuxS/M16.
DR   InterPro; IPR011765; Pept_M16_N.
DR   InterPro; IPR007863; Peptidase_M16_C.
DR   Pfam; PF00675; Peptidase_M16; 1.
DR   Pfam; PF05193; Peptidase_M16_C; 2.
DR   SUPFAM; SSF63411; SSF63411; 3.
PE   2: Evidence at transcript level;
KW   Alternative splicing; Chloroplast; Hydrolase; Metal-binding;
KW   Metalloprotease; Plastid; Protease; Reference proteome; Transit peptide;
KW   Zinc.
FT   TRANSIT         1..136
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000250|UniProtKB:Q40983"
FT   CHAIN           137..1246
FT                   /note="Stromal processing peptidase, chloroplastic"
FT                   /id="PRO_0000435735"
FT   ACT_SITE        231
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250|UniProtKB:Q40983"
FT   ACT_SITE        302
FT                   /evidence="ECO:0000305"
FT   BINDING         228
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q40983"
FT   BINDING         232
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000250|UniProtKB:Q40983"
FT   BINDING         309
FT                   /ligand="Zn(2+)"
FT                   /ligand_id="ChEBI:CHEBI:29105"
FT                   /evidence="ECO:0000305"
FT   VAR_SEQ         146..403
FT                   /note="Missing (in isoform 2)"
FT                   /id="VSP_058158"
SQ   SEQUENCE   1246 AA;  138685 MW;  0B170F9589482EE5 CRC64;
     MASFPSPPLA AAAAAAPPRL APGLPLAAAA VRRPSSLARR SSIALAAPAN PLRCIHRRAV
     SPRLRRRTEA VGAASAAIGS LGEEREGCLS CFPRGRRRGR PGLARFAPCA LPHTYGLSSL
     HSGLTGAKIR RRHVLHAAGP DEPHVASPTW SETALDKHYV DQPIGKEELE GFLNTPLPSH
     PKLVRGQLKN GLRYLILPNK VPANRFEAHM EVHVGSIDEE EDEQGIAHMI EHVAFLGSKK
     REKLLGTGAR SNAYTDFHHT VFHIHSPTKT KEYGEDLLPS VLDALNEIAF HPKFSSSRVE
     KERRAILSEL QMMNTIEYRV DCQLLQHLHS ENKLSERFPI GLEEQIHKWD PDKIRRFHER
     WYYPANATLY LVGEIDDIPR AIREIEAVFE HTLPEGEAAP MSTASPFGAM ASLFAPKLPG
     GLAASLTGER SPAADKIKPV KRERQAIRPP VEHKWSLPGV AQDAKPPAIF QHELIQSFSI
     NMFCKIPVNQ VQTYKDLRSV LMKRIFLSAL HFRINTRYKS SNPPFTSVEL DHSDSGREGC
     TVTTLTVTAE PQNWRSAIKV AVHEVRRLKE FGVTMGEMTR YMDALIKDSE QLAMMIDSVP
     SVDNLDFIME SDALRHTVMD QLQGHESLLA VAETVTLEEV NTVGAEVLEF ISDYGKPDAP
     LPAAIVACVP KKVHMDGVGE TDFEIHPEEI TDSIKAGLEE PIYPEPELEV PKELITRSEL
     EDLKLQRKPS FASLSKEENV VKIFDDETGI AQRRLSNGIS INYKITQNEA RVGVMRLIVG
     GGRATEDSES KGSVIVGVRT LSEGGCVGNF SREQVELFCV NNLINCSLES NEEFIFMEFR
     FALRDNGMRA AFQLLHMVLE HNVWLEDAFD RATQLYLSYY RSIPKSLERS TAHKLMLAML
     NHDERFVEPS PHSLQKLTLQ SVKDAVMNQF VGDNMEVSIV GDFTEEEVES CVLDYLGTVS
     APKSSKTQEH IEKISFLPFP SDLHFQQVYI KDTDERACAY IAGPAPNRWG FATEGNDLFN
     VIRSSSGDAQ VSESANTDLT ERKHNDVRSH SLFFGITLSL LAEIINSRLF TTVRDSMGLT
     YDVSFELNLF DKLDLGWYVI AVTSTPSKVH KAVDACKGVL RGLHSNKIVE RELDRAKRTL
     LMKHEAETKT NAYWLGLLAH LQSSSVPRKE ISCIKELTML YESATIEDLY LAYEHLKVDE
     SSLFACIGIA GAESGEETTD DELDMGLHGM GPIGGRGLST MTRPTT