AMY1_ORYSJ
ID AMY1_ORYSJ Reviewed; 434 AA.
AC P17654; Q6Z317;
DT 01-AUG-1990, integrated into UniProtKB/Swiss-Prot.
DT 25-OCT-2005, sequence version 2.
DT 03-AUG-2022, entry version 158.
DE RecName: Full=Alpha-amylase;
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 1B;
DE Flags: Precursor;
GN Name=AMY1.1; Synonyms=AMY1A;
GN OrderedLocusNames=Os02g0765600, LOC_Os02g52710;
GN ORFNames=OJ1004_A11.13, P0539D10.32;
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 [MRNA].
RC STRAIN=cv. M202;
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 [2]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=cv. M202;
RX PubMed=2102847; DOI=10.1007/bf00016499;
RA Huang N., Sutliff T.D., Litts J.C., Rodriguez R.L.;
RT "Classification and characterization of the rice alpha-amylase multigene
RT family.";
RL Plant Mol. Biol. 14:655-668(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: More abundant in germinating seeds, than in callus,
CC young roots and leaves.
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 -!- PTM: Only cereal amylase known to be glycosylated.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CAA34516.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; M24286; AAA33885.1; -; mRNA.
DR EMBL; X16509; CAA34516.1; ALT_INIT; Genomic_DNA.
DR EMBL; AP004817; BAD17125.1; -; Genomic_DNA.
DR EMBL; AP005287; BAD17313.1; -; Genomic_DNA.
DR EMBL; AP014958; BAS81060.1; -; Genomic_DNA.
DR PIR; S10013; S10013.
DR PIR; S12775; S12775.
DR RefSeq; XP_015622769.1; XM_015767283.1.
DR PDB; 3WN6; X-ray; 2.16 A; A/B/C/D=31-434.
DR PDBsum; 3WN6; -.
DR AlphaFoldDB; P17654; -.
DR SMR; P17654; -.
DR STRING; 4530.OS02T0765600-01; -.
DR CAZy; GH13; Glycoside Hydrolase Family 13.
DR GlyConnect; 24; 10 N-Linked glycans.
DR PaxDb; P17654; -.
DR PRIDE; P17654; -.
DR EnsemblPlants; Os02t0765600-01; Os02t0765600-01; Os02g0765600.
DR GeneID; 4330832; -.
DR Gramene; Os02t0765600-01; Os02t0765600-01; Os02g0765600.
DR KEGG; osa:4330832; -.
DR eggNOG; KOG0471; Eukaryota.
DR HOGENOM; CLU_030069_1_0_1; -.
DR InParanoid; P17654; -.
DR OMA; GEQGYMP; -.
DR OrthoDB; 665362at2759; -.
DR BRENDA; 3.2.1.1; 4460.
DR Proteomes; UP000000763; Chromosome 2.
DR Proteomes; UP000059680; Chromosome 2.
DR ExpressionAtlas; P17654; baseline and differential.
DR Genevisible; P17654; 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 1: Evidence at protein level;
KW 3D-structure; Calcium; Carbohydrate metabolism; Glycoprotein; Glycosidase;
KW Hydrolase; Metal-binding; Reference proteome; Signal.
FT SIGNAL 1..31
FT /evidence="ECO:0000305"
FT CHAIN 32..434
FT /note="Alpha-amylase"
FT /id="PRO_0000001408"
FT ACT_SITE 209
FT /note="Nucleophile"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT ACT_SITE 234
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 75..77
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 82..83
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 122
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
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 142
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 144
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 148
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 158
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="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 171
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 172
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="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 176
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 178
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 178
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="3"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 207..212
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 213
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 236
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 238
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P04063"
FT BINDING 256
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 263
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 300
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 306..308
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 319
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 325
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 404
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 409..411
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 421..427
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT BINDING 431
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT SITE 320
FT /note="Transition state stabilizer"
FT /evidence="ECO:0000250|UniProtKB:P00693"
FT CARBOHYD 271
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000305"
FT CONFLICT 272
FT /note="A -> G (in Ref. 1; AAA33885 and 2; CAA34516)"
FT /evidence="ECO:0000305"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 42..44
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 49..54
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 57..62
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 67..70
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 76..78
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 81..84
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 90..92
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 98..110
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 127..129
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 141..145
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 151..153
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 184..199
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 205..208
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 211..213
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 216..226
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 231..233
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 245..247
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 252..264
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 267..269
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 272..275
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 277..286
FT /evidence="ECO:0007829|PDB:3WN6"
FT TURN 287..289
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 291..294
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 304..306
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 309..311
FT /evidence="ECO:0007829|PDB:3WN6"
FT TURN 319..321
FT /evidence="ECO:0007829|PDB:3WN6"
FT TURN 323..325
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 332..334
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 335..344
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 345..347
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 350..352
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 353..357
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 362..374
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 383..389
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 392..397
FT /evidence="ECO:0007829|PDB:3WN6"
FT TURN 398..400
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 401..407
FT /evidence="ECO:0007829|PDB:3WN6"
FT HELIX 412..414
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 419..425
FT /evidence="ECO:0007829|PDB:3WN6"
FT STRAND 428..433
FT /evidence="ECO:0007829|PDB:3WN6"
SQ SEQUENCE 434 AA; 48457 MW; 7B23B299A0AD3E37 CRC64;
MQVLNTMVNK HFLSLSVLIV LLGLSSNLTA GQVLFQGFNW ESWKENGGWY NFLMGKVDDI
AAAGITHVWL PPPSHSVGEQ GYMPGRLYDL DASKYGNEAQ LKSLIEAFHG KGVQVIADIV
INHRTAEHKD GRGIYCLFEG GTPDSRLDWG PHMICRDDPY GDGTGNPDTG ADFAAAPDID
HLNKRVQREL IGWLDWLKMD IGFDAWRLDF AKGYSADMAK IYIDATEPSF AVAEIWTSMA
NGGDGKPNYD QNAHRQELVN WVDRVGGANS NATAFDFTTK GILNVAVEGE LWRLRGEDGK
APGMIGWWPA KATTFVDNHD TGSTQHLWPF PSDKVMQGYA YILTHPGNPC IFYDHFFDWG
LKEEIERLVS IRNRQGIHPA SELRIMEADS DLYLAEIDGK VITKIGPRYD VEHLIPEGFQ
VVAHGDGYAI WEKI
