AMY3D_ORYSJ
ID AMY3D_ORYSJ Reviewed; 436 AA.
AC P27933; Q6ZDD5;
DT 01-AUG-1992, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 2.
DT 03-AUG-2022, entry version 135.
DE RecName: Full=Alpha-amylase isozyme 3D;
DE EC=3.2.1.1 {ECO:0000250|UniProtKB:P00693};
DE AltName: Full=1,4-alpha-D-glucan glucanohydrolase;
DE Flags: Precursor;
GN Name=AMY1.3; Synonyms=AMY3D;
GN OrderedLocusNames=Os08g0473900, LOC_Os08g36910;
GN ORFNames=P0013B04.36-1, P0451G12.5-1;
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; TISSUE=Etiolated leaf;
RX PubMed=2263460; DOI=10.1093/nar/18.23.7007;
RA Huang N., Koizumi N., Reinl S.J., Rodriguez R.L.;
RT "Structural organization and differential expression of rice alpha-amylase
RT genes.";
RL Nucleic Acids Res. 18:7007-7014(1990).
RN [2]
RP NUCLEOTIDE SEQUENCE [MRNA].
RX PubMed=2370848; DOI=10.1007/bf00261726;
RA O'Neill S.D., Kumagai M.H., Majumdar A., Huang N., Sutliff T.D.,
RA Rodriguez R.L.;
RT "The alpha-amylase genes in Oryza sativa: characterization of cDNA clones
RT and mRNA expression during seed germination.";
RL Mol. Gen. Genet. 221:235-244(1990).
RN [3]
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 [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).
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.
CC -!- TISSUE SPECIFICITY: Is expressed in all tissues, except in immature
CC seeds. Is the most abundant alpha-amylase isozyme in callus.
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; M59351; AAA33895.1; -; Genomic_DNA.
DR EMBL; M24287; AAA33886.1; -; mRNA.
DR EMBL; AP004399; BAD09335.1; -; Genomic_DNA.
DR EMBL; AP004457; BAD09375.1; -; Genomic_DNA.
DR EMBL; AP014964; BAT05862.1; -; Genomic_DNA.
DR PIR; S12625; S12625.
DR AlphaFoldDB; P27933; -.
DR SMR; P27933; -.
DR STRING; 4530.OS08T0473900-01; -.
DR CAZy; GH13; Glycoside Hydrolase Family 13.
DR PaxDb; P27933; -.
DR EnsemblPlants; Os08t0473900-02; Os08t0473900-02; Os08g0473900.
DR Gramene; Os08t0473900-02; Os08t0473900-02; Os08g0473900.
DR eggNOG; KOG0471; Eukaryota.
DR InParanoid; P27933; -.
DR Proteomes; UP000000763; Chromosome 8.
DR Proteomes; UP000059680; Chromosome 8.
DR ExpressionAtlas; P27933; baseline and differential.
DR Genevisible; P27933; 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; IEP:Gramene.
DR GO; GO:0005987; P:sucrose catabolic process; IEP:Gramene.
DR Gene3D; 2.60.40.1180; -; 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 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; SSF51445; 1.
PE 2: Evidence at transcript level;
KW Calcium; Carbohydrate metabolism; Glycosidase; Hydrolase; Metal-binding;
KW Reference proteome; Signal.
FT SIGNAL 1..25
FT /evidence="ECO:0000255"
FT CHAIN 26..436
FT /note="Alpha-amylase isozyme 3D"
FT /id="PRO_0000001415"
FT ACT_SITE 204
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT ACT_SITE 229
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 69..71
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 76..77
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 116
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
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 136
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 138
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 142
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 152
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
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 168
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 171
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 173
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 173
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 202..207
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 208
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 231
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 233
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 251
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 292
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 298..300
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 311
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 317
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 396
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 401..403
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 413..419
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 423
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT SITE 312
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT CONFLICT 73..74
FT /note="PQ -> R (in Ref. 2; AAA33886)"
FT /evidence="ECO:0000305"
FT CONFLICT 137
FT /note="P -> R (in Ref. 2; AAA33886)"
FT /evidence="ECO:0000305"
FT CONFLICT 138
FT /note="Missing (in Ref. 1; AAA33895 and 2; AAA33886)"
FT /evidence="ECO:0000305"
FT CONFLICT 294
FT /note="A -> P (in Ref. 1; AAA33895 and 2; AAA33886)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 436 AA; 48000 MW; D353346D13D3DC93 CRC64;
MKNTSSLCLL LLVVLCSLTC NSGQAQVLFQ GFNWESWKQQ GGWYNMLKGQ VDDIAKAGVT
HVWLPPPSHS VAPQGYMPGR LYDLDASKYG TAAELKSLIA AFHGKGVQCV ADVVINHRCA
EKKDARGVYC VFEGGTPDDR LDWGPGMICS DDTQYSDGTG HRDTGEGFGA APDIDHLNPR
VQRELTDWLN WLKSDVGFDG WRLDFAKGYS TDIAKMYVES CKPGFVVAEI WNSLSYNGDG
KPAANQDQGR QELVNWVNAV GGPAMTFDFT TKGLLQAGVQ GELWRLRDGN GKAAGMIGWL
PEKAVTFVDN HDTGSTQKLW PFPSDKVMQG YAYILTHPGV PCIFYDHMFD WNLKQEITAL
AAIRERNGIN AGSKLRIVVA DADAYVAVVD EKVMVKIGTR YDVGNAVPSD FHQTVHGKDY
SVWEKGSLRV PAGRHL
