ID AMY2A_ORYSJ Reviewed; 445 AA.
AC Q0D9J1; B7E3X5; P27935; P27941; Q5Z7T8;
DT 12-JUN-2007, integrated into UniProtKB/Swiss-Prot.
DT 17-OCT-2006, sequence version 1.
DT 27-MAR-2024, entry version 107.
DE RecName: Full=Alpha-amylase isozyme 2A;
DE EC=3.2.1.1 {ECO:0000250|UniProtKB:P00693};
DE AltName: Full=1,4-alpha-D-glucan glucanohydrolase;
DE AltName: Full=Alpha-amylase isozyme C2;
DE Flags: Precursor;
GN Name=AMY2A; Synonyms=AMY1.5, AMYC2;
GN OrderedLocusNames=Os06g0713800, LOC_Os06g49970;
GN ORFNames=OJ1136_F03.12, OsJ_22644 {ECO:0000312|EMBL:EEE66350.1};
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 [GENOMIC DNA].
RC STRAIN=cv. M202;
RX PubMed=1541400; DOI=10.1016/0378-1119(92)90690-q;
RA Huang N., Reinl S.J., Rodriguez R.L.;
RT "RAmy2A; a novel alpha-amylase-encoding gene in rice.";
RL Gene 111:223-228(1992).
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).
RN [6]
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 -!- FUNCTION: Important for breakdown of endosperm starch during
CC germination.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in
CC polysaccharides containing three or more (1->4)-alpha-linked D-
CC glucose units.; EC=3.2.1.1; Evidence={ECO:0000250|UniProtKB:P00693};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:P00693};
CC Note=Binds 3 Ca(2+) ions per subunit. {ECO:0000250|UniProtKB:P00693};
CC -!- SUBUNIT: Monomer. {ECO:0000250}.
CC -!- DEVELOPMENTAL STAGE: Expressed at a high level during germination in
CC the aleurones cells under the control of the plant hormone gibberellic
CC acid and in the developing grains at a low level.
CC -!- MISCELLANEOUS: Binds starch not only at the active site, but also via
CC accessory binding sites on the protein surface that are important for
CC efficient binding to starch granules and thereby increase enzyme
CC activity. {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the glycosyl hydrolase 13 family. {ECO:0000305}.
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DR EMBL; M74177; AAA33894.1; -; Genomic_DNA.
DR EMBL; AP004678; BAD54103.1; -; Genomic_DNA.
DR EMBL; AP008212; BAF20482.1; -; Genomic_DNA.
DR EMBL; AP014962; BAS99475.1; -; Genomic_DNA.
DR EMBL; CM000143; EEE66350.1; -; Genomic_DNA.
DR EMBL; AK059671; BAG87072.1; -; mRNA.
DR EMBL; AK101018; BAG94883.1; -; mRNA.
DR PIR; JQ1527; JQ1527.
DR RefSeq; XP_015641245.1; XM_015785759.1.
DR AlphaFoldDB; Q0D9J1; -.
DR SMR; Q0D9J1; -.
DR STRING; 39947.Q0D9J1; -.
DR CAZy; GH13; Glycoside Hydrolase Family 13.
DR PaxDb; 39947-Q0D9J1; -.
DR EnsemblPlants; Os06t0713800-01; Os06t0713800-01; Os06g0713800.
DR GeneID; 4342055; -.
DR Gramene; Os06t0713800-01; Os06t0713800-01; Os06g0713800.
DR KEGG; osa:4342055; -.
DR eggNOG; KOG0471; Eukaryota.
DR HOGENOM; CLU_030069_1_0_1; -.
DR InParanoid; Q0D9J1; -.
DR OMA; AVWEKSA; -.
DR OrthoDB; 201664at2759; -.
DR Proteomes; UP000000763; Chromosome 6.
DR Proteomes; UP000007752; Chromosome 6.
DR Proteomes; UP000059680; Chromosome 6.
DR Genevisible; Q0D9J1; OS.
DR GO; GO:0004556; F:alpha-amylase activity; IBA:GO_Central.
DR GO; GO:0005509; F:calcium ion binding; IEA:InterPro.
DR GO; GO:0005983; P:starch catabolic process; IEA:UniProt.
DR GO; GO:0005987; P:sucrose catabolic process; IBA:GO_Central.
DR CDD; cd11314; AmyAc_arch_bac_plant_AmyA; 1.
DR Gene3D; 3.20.20.80; Glycosidases; 1.
DR Gene3D; 2.60.40.1180; Golgi alpha-mannosidase II; 1.
DR InterPro; IPR012850; A-amylase_bs_C.
DR InterPro; IPR013775; A-amylase_pln.
DR InterPro; IPR006046; Alpha_amylase.
DR InterPro; IPR006047; Glyco_hydro_13_cat_dom.
DR InterPro; IPR013780; Glyco_hydro_b.
DR InterPro; IPR017853; Glycoside_hydrolase_SF.
DR PANTHER; PTHR43447; ALPHA-AMYLASE; 1.
DR PANTHER; PTHR43447:SF38; ALPHA-AMYLASE ISOZYME 2A; 1.
DR Pfam; PF07821; Alpha-amyl_C2; 1.
DR Pfam; PF00128; Alpha-amylase; 1.
DR PIRSF; PIRSF001028; Alph-amls_plant; 1.
DR PRINTS; PR00110; ALPHAAMYLASE.
DR SMART; SM00642; Aamy; 1.
DR SMART; SM00810; Alpha-amyl_C2; 1.
DR SUPFAM; SSF51445; (Trans)glycosidases; 1.
DR SUPFAM; SSF51011; Glycosyl hydrolase domain; 1.
PE 2: Evidence at transcript level;
KW Calcium; Carbohydrate metabolism; Glycosidase; Hydrolase; Metal-binding;
KW Reference proteome; Signal.
FT SIGNAL 1..21
FT /evidence="ECO:0000255"
FT CHAIN 22..445
FT /note="Alpha-amylase isozyme 2A"
FT /id="PRO_0000001409"
FT ACT_SITE 202
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT ACT_SITE 228
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 66..68
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 73..74
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 113
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 130
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 133
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 135
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 139
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 149
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 160
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 163
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 164
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 165
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 168
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 170
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 170
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 200..205
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 206
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 230
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 232
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 250
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 257
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 294
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 300..302
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 313
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 319
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 398
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 403..405
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 415..421
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 425
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT SITE 314
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT CONFLICT 428..430
FT /note="IAA -> S (in Ref. 1; AAA33894)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 445 AA; 48696 MW; D7D61EC6DB04445E CRC64;
MATGRRLSMI LLLLLLGLAS GDKILFQGFN WESWRQSGGW YNLLMGKVDD IVAAGVTHVW
LPPPSHSVST QGYMPGRLYD LDASRYGTSM ELKSLISALH GKGIQAIADV VINHRCADYK
DSRGIYCIFE GGTPDGRLDW GPHMICRDDT QFSDGTGNLD TGADFAAAPD IDHLNGVVQR
ELTDWLLWLK SDEVGFDAWR LDFARGYSPE VAKVYIEGTT PVGLAVAELW DSMAYGGDGK
PEYNQDAHRQ ALVDWVDRVG GTASAGMVFD FTTKGIMNTA VEGELWRLID QQGKAPGVIG
WWPAKAVTFV DNHDTGSTQQ MWPFPSDKVM QGYAYILTHP GNPCIFYDHF FDWGLKEQIA
ALVAVRQRNG VTATSSLKIM LHDADAYVAE IDGKVVMKIG SRYDVSSLIP PGFHLAAHGN
GYAVWEKIAA AAAAADHRTS SSASL
//
