ID   ISOA3_ORYSJ             Reviewed;         782 AA.
AC   B9G434; A0A0P0XN30; Q0J118; Q6K4A4;
DT   25-OCT-2017, integrated into UniProtKB/Swiss-Prot.
DT   24-MAR-2009, sequence version 1.
DT   03-AUG-2022, entry version 75.
DE   RecName: Full=Isoamylase 3, chloroplastic {ECO:0000305};
DE            Short=OsISA3 {ECO:0000303|PubMed:15618430};
DE            EC=3.2.1.68 {ECO:0000269|PubMed:21551159};
DE   Flags: Precursor;
GN   Name=ISA3 {ECO:0000303|PubMed:15618430};
GN   OrderedLocusNames=Os09g0469400 {ECO:0000312|EMBL:BAT08543.1},
GN   LOC_Os09g29404 {ECO:0000305};
GN   ORFNames=OJ1595_D08.13-1 {ECO:0000312|EMBL:BAD22265.1},
GN   OsJ_29702 {ECO:0000312|EMBL:EEE69882.1},
GN   P0676H02.31-1 {ECO:0000312|EMBL:BAD19754.1};
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] OF 406-782.
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).
RN   [6]
RP   TISSUE SPECIFICITY.
RX   PubMed=15618430; DOI=10.1104/pp.104.051359;
RA   Kubo A., Rahman S., Utsumi Y., Li Z., Mukai Y., Yamamoto M., Ugaki M.,
RA   Harada K., Satoh H., Konik-Rose C., Morell M., Nakamura Y.;
RT   "Complementation of sugary-1 phenotype in rice endosperm with the wheat
RT   isoamylase1 gene supports a direct role for isoamylase1 in amylopectin
RT   biosynthesis.";
RL   Plant Physiol. 137:43-56(2005).
RN   [7]
RP   FUNCTION, AND SUBCELLULAR LOCATION.
RX   PubMed=21551159; DOI=10.1093/pcp/pcr058;
RA   Yun M.S., Umemoto T., Kawagoe Y.;
RT   "Rice debranching enzyme isoamylase3 facilitates starch metabolism and
RT   affects plastid morphogenesis.";
RL   Plant Cell Physiol. 52:1068-1082(2011).
CC   -!- FUNCTION: Starch-debranching enzyme that plays a role in the
CC       degradation of transitory starch during the night in leaf blades,
CC       facilitates the formation of spherical amyloplasts containing compound
CC       granules in the endosperm, and affects morphological characteristics of
CC       plastids. {ECO:0000269|PubMed:21551159}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=Hydrolysis of (1->6)-alpha-D-glucosidic branch linkages in
CC         glycogen, amylopectin and their beta-limit dextrins.; EC=3.2.1.68;
CC         Evidence={ECO:0000269|PubMed:21551159};
CC   -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000255}. Plastid,
CC       amyloplast {ECO:0000269|PubMed:21551159}. Note=Localizes in amyloplast
CC       stroma of seed endosperm. {ECO:0000269|PubMed:21551159}.
CC   -!- TISSUE SPECIFICITY: Expressed in leaves. Expressed at low levels in
CC       developing endosperm. {ECO:0000269|PubMed:15618430}.
CC   -!- SIMILARITY: Belongs to the glycosyl hydrolase 13 family. {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=BAD19754.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAD22265.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAF25347.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=BAT08543.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AP005399; BAD19754.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP005574; BAD22265.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP008215; BAF25347.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AP014965; BAT08543.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CM000146; EEE69882.1; -; Genomic_DNA.
DR   EMBL; AK101554; BAG95120.1; -; mRNA.
DR   RefSeq; XP_015612255.1; XM_015756769.1.
DR   AlphaFoldDB; B9G434; -.
DR   SMR; B9G434; -.
DR   STRING; 4530.OS09T0469400-01; -.
DR   CAZy; CBM48; Carbohydrate-Binding Module Family 48.
DR   CAZy; GH13; Glycoside Hydrolase Family 13.
DR   PRIDE; B9G434; -.
DR   GeneID; 4347328; -.
DR   KEGG; osa:4347328; -.
DR   eggNOG; KOG0470; Eukaryota.
DR   HOGENOM; CLU_063553_0_0_1; -.
DR   OrthoDB; 533388at2759; -.
DR   Proteomes; UP000000763; Chromosome 9.
DR   Proteomes; UP000007752; Chromosome 9.
DR   Proteomes; UP000059680; Chromosome 9.
DR   GO; GO:0009501; C:amyloplast; IDA:UniProtKB.
DR   GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR   GO; GO:0019156; F:isoamylase activity; IDA:UniProtKB.
DR   GO; GO:0009660; P:amyloplast organization; IMP:UniProtKB.
DR   GO; GO:0019252; P:starch biosynthetic process; IEA:UniProtKB-KW.
DR   GO; GO:0005983; P:starch catabolic process; IDA:UniProtKB.
DR   CDD; cd02856; E_set_GDE_Isoamylase_N; 1.
DR   Gene3D; 2.60.40.10; -; 1.
DR   Gene3D; 2.60.40.1180; -; 1.
DR   InterPro; IPR044505; GlgX_Isoamylase_N_E_set.
DR   InterPro; IPR006047; Glyco_hydro_13_cat_dom.
DR   InterPro; IPR004193; Glyco_hydro_13_N.
DR   InterPro; IPR013780; Glyco_hydro_b.
DR   InterPro; IPR017853; Glycoside_hydrolase_SF.
DR   InterPro; IPR013783; Ig-like_fold.
DR   InterPro; IPR014756; Ig_E-set.
DR   Pfam; PF00128; Alpha-amylase; 1.
DR   Pfam; PF02922; CBM_48; 1.
DR   SMART; SM00642; Aamy; 1.
DR   SUPFAM; SSF51445; SSF51445; 1.
DR   SUPFAM; SSF81296; SSF81296; 1.
PE   2: Evidence at transcript level;
KW   Amyloplast; Carbohydrate metabolism; Chloroplast; Glycosidase; Hydrolase;
KW   Plastid; Reference proteome; Starch biosynthesis; Transit peptide.
FT   TRANSIT         1..68
FT                   /note="Chloroplast"
FT                   /evidence="ECO:0000255"
FT   CHAIN           69..782
FT                   /note="Isoamylase 3, chloroplastic"
FT                   /id="PRO_0000441800"
FT   REGION          68..88
FT                   /note="Disordered"
FT                   /evidence="ECO:0000256|SAM:MobiDB-lite"
FT   ACT_SITE        445
FT                   /note="Nucleophile"
FT                   /evidence="ECO:0000250|UniProtKB:P04746"
FT   ACT_SITE        482
FT                   /note="Proton donor"
FT                   /evidence="ECO:0000250|UniProtKB:P04746"
FT   SITE            555
FT                   /note="Transition state stabilizer"
FT                   /evidence="ECO:0000250|UniProtKB:P04746"
SQ   SEQUENCE   782 AA;  87533 MW;  ECAE1EC739A28478 CRC64;
     MDSIGINRAP LGSSSSAAAV TARRGIALRP ARRSVASTNR VGVATIGFGD ASGLRACSEK
     VRRFDSVRST TARAQNGNAG RSMTEERGCT MSDTEMPFKY SSGKAFPLGV SQVEGGLNFA
     LFSQHASSVI LCLKLPGRGT EDEKGADVVE FVLDQQKNKT GDIWHVIVEG LPASGVLYGY
     RVGGPQGWDQ GHRFDSSTVL LDPYAKLVSG RKYFGVAEEK SSQHFGTYDF DSSPFDWGDD
     YRLPNLPEAD LVIYEMNVRA FTADESSGLD STSRGSYLGL IDKIPHLLEL GVNAVELLPV
     FEYDELEFKR YPNPRDHMVN TWGYSTINFF APMSRYASAG GGPVAASKEL KQMVKELHKA
     GIEVILDVVY NHTNEADDAH PYMTSFRGID NKVYYMLDLN KNAELLNFSG CGNTLNCNHP
     VVKELILDSL RHWVEEYHID GFRFDLASVL CRGPDGCPLD APPLIKEIAK DAVLSRCKII
     AEPWDCGGLY LVGRFPNWDR WAEWNGKYRD DLRRFIKGDP GMKGVFATRV SGSADLYQVN
     ERKPYHGVNF VIAHDGFTLC DLVSYNLKHN DANGEGGCDG CNDNFSWNCG VEGETNDLNV
     LSLRSRQMKN FHVALMISQG TPMMLMGDEY GHTRYGNNNS YGHDTCINNF QWEQLEQRRD
     GHFRFFSEMI KFRHSNPILR RDRFLNKNDV TWHEDCWENQ ESKFLAFTVH DHNSGGDIYL
     AFNAHDYFVD AVIPPPPHHK CWNRVVDTNL ESPNDIVPEG VPFTGPKYRI APYSSILLKA
     KP