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Protein

Alpha-amylase

Gene

AMY1.1

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Important for breakdown of endosperm starch during germination.

Catalytic activityi

Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units.By similarity

Cofactori

Ca2+By similarityNote: Binds 3 Ca2+ ions per subunit.By similarity

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi122 – 1221Calcium 1By similarity
Metal bindingi139 – 1391Calcium 2By similarity
Metal bindingi142 – 1421Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi144 – 1441Calcium 2; via carbonyl oxygenBy similarity
Metal bindingi148 – 1481Calcium 2By similarity
Metal bindingi158 – 1581Calcium 3By similarity
Metal bindingi168 – 1681Calcium 1By similarity
Metal bindingi171 – 1711Calcium 1; via carbonyl oxygenBy similarity
Metal bindingi172 – 1721Calcium 3By similarity
Metal bindingi173 – 1731Calcium 3; via carbonyl oxygenBy similarity
Metal bindingi176 – 1761Calcium 3; via carbonyl oxygenBy similarity
Metal bindingi178 – 1781Calcium 1By similarity
Metal bindingi178 – 1781Calcium 3By similarity
Active sitei209 – 2091NucleophileBy similarity
Metal bindingi213 – 2131Calcium 1; via carbonyl oxygenBy similarity
Active sitei234 – 2341Proton donorBy similarity
Binding sitei236 – 2361SubstrateBy similarity
Binding sitei238 – 2381SubstrateBy similarity
Binding sitei256 – 2561SubstrateBy similarity
Binding sitei263 – 2631SubstrateBy similarity
Binding sitei300 – 3001SubstrateBy similarity
Binding sitei319 – 3191SubstrateBy similarity
Sitei320 – 3201Transition state stabilizerBy similarity
Binding sitei325 – 3251SubstrateBy similarity
Binding sitei404 – 4041SubstrateBy similarity
Binding sitei431 – 4311SubstrateBy similarity

GO - Molecular functioni

GO - Biological processi

  • starch catabolic process Source: Gramene
  • sucrose catabolic process Source: Gramene
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.2.1.1. 4460.

Protein family/group databases

CAZyiGH13. Glycoside Hydrolase Family 13.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-amylase (EC:3.2.1.1By similarity)
Alternative name(s):
1,4-alpha-D-glucan glucanohydrolase
Alpha-amylase isozyme 1B
Gene namesi
Name:AMY1.1
Synonyms:AMY1A
Ordered Locus Names:Os02g0765600, LOC_Os02g52710
ORF Names:OJ1004_A11.13, P0539D10.32
OrganismiOryza sativa subsp. japonica (Rice)
Taxonomic identifieri39947 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryza
Proteomesi
  • UP000059680 Componenti: Chromosome 2, cultivar: Nipponbare

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 3131CuratedAdd
BLAST
Chaini32 – 434403Alpha-amylasePRO_0000001408Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi271 – 2711N-linked (GlcNAc...)Curated

Post-translational modificationi

Only cereal amylase known to be glycosylated.

Keywords - PTMi

Glycoprotein

Proteomic databases

PaxDbiP17654.

Expressioni

Tissue specificityi

More abundant in germinating seeds, than in callus, young roots and leaves.

Developmental stagei

Expressed at a high level during germination in the aleurones cells under the control of the plant hormone gibberellic acid and in the developing grains at a low level.

Gene expression databases

ExpressionAtlasiP17654. baseline and differential.
GenevisibleiP17654. OS.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

STRINGi39947.LOC_Os02g52710.1.

Structurei

Secondary structure

1
434
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi34 – 363Combined sources
Helixi42 – 443Combined sources
Helixi49 – 546Combined sources
Helixi57 – 626Combined sources
Beta strandi67 – 704Combined sources
Beta strandi76 – 783Combined sources
Beta strandi81 – 844Combined sources
Helixi90 – 923Combined sources
Helixi98 – 11013Combined sources
Beta strandi114 – 1196Combined sources
Beta strandi127 – 1293Combined sources
Beta strandi135 – 1373Combined sources
Beta strandi141 – 1455Combined sources
Helixi151 – 1533Combined sources
Helixi184 – 19916Combined sources
Beta strandi205 – 2084Combined sources
Helixi211 – 2133Combined sources
Helixi216 – 22611Combined sources
Beta strandi231 – 2333Combined sources
Beta strandi245 – 2473Combined sources
Helixi252 – 26413Combined sources
Helixi267 – 2693Combined sources
Beta strandi272 – 2754Combined sources
Helixi277 – 28610Combined sources
Turni287 – 2893Combined sources
Helixi291 – 2944Combined sources
Helixi304 – 3063Combined sources
Helixi309 – 3113Combined sources
Turni319 – 3213Combined sources
Turni323 – 3253Combined sources
Helixi332 – 3343Combined sources
Helixi335 – 34410Combined sources
Beta strandi345 – 3473Combined sources
Beta strandi350 – 3523Combined sources
Helixi353 – 3575Combined sources
Helixi362 – 37413Combined sources
Beta strandi383 – 3897Combined sources
Beta strandi392 – 3976Combined sources
Turni398 – 4003Combined sources
Beta strandi401 – 4077Combined sources
Helixi412 – 4143Combined sources
Beta strandi419 – 4257Combined sources
Beta strandi428 – 4336Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3WN6X-ray2.16A/B/C/D31-434[»]
ProteinModelPortaliP17654.
SMRiP17654. Positions 32-434.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 773Substrate bindingBy similarity
Regioni82 – 832Substrate bindingBy similarity
Regioni207 – 2126Substrate bindingBy similarity
Regioni306 – 3083Substrate bindingBy similarity
Regioni409 – 4113Substrate bindingBy similarity
Regioni421 – 4277Substrate bindingBy similarity

Sequence similaritiesi

Belongs to the glycosyl hydrolase 13 family.Curated

Keywords - Domaini

Signal

Phylogenomic databases

eggNOGiKOG0471. Eukaryota.
COG0366. LUCA.
HOGENOMiHOG000239525.
InParanoidiP17654.
KOiK01176.
OMAiGEQGYMP.

Family and domain databases

Gene3Di2.60.40.1180. 1 hit.
3.20.20.80. 1 hit.
InterProiIPR012850. A-amylase_bs_C.
IPR013775. A-amylase_pln.
IPR006046. Alpha_amylase.
IPR015902. Glyco_hydro_13.
IPR006047. Glyco_hydro_13_cat_dom.
IPR013780. Glyco_hydro_b.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PANTHERiPTHR10357. PTHR10357. 1 hit.
PfamiPF07821. Alpha-amyl_C2. 1 hit.
PF00128. Alpha-amylase. 1 hit.
[Graphical view]
PIRSFiPIRSF001028. Alph-amls_plant. 1 hit.
PRINTSiPR00110. ALPHAAMYLASE.
SMARTiSM00642. Aamy. 1 hit.
SM00810. Alpha-amyl_C2. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

P17654-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MQVLNTMVNK HFLSLSVLIV LLGLSSNLTA GQVLFQGFNW ESWKENGGWY
60 70 80 90 100
NFLMGKVDDI AAAGITHVWL PPPSHSVGEQ GYMPGRLYDL DASKYGNEAQ
110 120 130 140 150
LKSLIEAFHG KGVQVIADIV INHRTAEHKD GRGIYCLFEG GTPDSRLDWG
160 170 180 190 200
PHMICRDDPY GDGTGNPDTG ADFAAAPDID HLNKRVQREL IGWLDWLKMD
210 220 230 240 250
IGFDAWRLDF AKGYSADMAK IYIDATEPSF AVAEIWTSMA NGGDGKPNYD
260 270 280 290 300
QNAHRQELVN WVDRVGGANS NATAFDFTTK GILNVAVEGE LWRLRGEDGK
310 320 330 340 350
APGMIGWWPA KATTFVDNHD TGSTQHLWPF PSDKVMQGYA YILTHPGNPC
360 370 380 390 400
IFYDHFFDWG LKEEIERLVS IRNRQGIHPA SELRIMEADS DLYLAEIDGK
410 420 430
VITKIGPRYD VEHLIPEGFQ VVAHGDGYAI WEKI
Length:434
Mass (Da):48,457
Last modified:October 25, 2005 - v2
Checksum:i7B23B299A0AD3E37
GO

Sequence cautioni

The sequence CAA34516.1 differs from that shown. Reason: Erroneous initiation. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti272 – 2721A → G in AAA33885 (PubMed:2370848).Curated
Sequence conflicti272 – 2721A → G in CAA34516 (PubMed:2102847).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24286 mRNA. Translation: AAA33885.1.
X16509 Genomic DNA. Translation: CAA34516.1. Different initiation.
AP004817 Genomic DNA. Translation: BAD17125.1.
AP005287 Genomic DNA. Translation: BAD17313.1.
AP014958 Genomic DNA. Translation: BAS81060.1.
PIRiS10013.
S12775.
RefSeqiXP_015622769.1. XM_015767283.1.
UniGeneiOs.49249.

Genome annotation databases

EnsemblPlantsiOS02T0765600-01; OS02T0765600-01; OS02G0765600.
GeneIDi4330832.
GrameneiOS02T0765600-01; OS02T0765600-01; OS02G0765600.
KEGGiosa:4330832.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
M24286 mRNA. Translation: AAA33885.1.
X16509 Genomic DNA. Translation: CAA34516.1. Different initiation.
AP004817 Genomic DNA. Translation: BAD17125.1.
AP005287 Genomic DNA. Translation: BAD17313.1.
AP014958 Genomic DNA. Translation: BAS81060.1.
PIRiS10013.
S12775.
RefSeqiXP_015622769.1. XM_015767283.1.
UniGeneiOs.49249.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
3WN6X-ray2.16A/B/C/D31-434[»]
ProteinModelPortaliP17654.
SMRiP17654. Positions 32-434.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi39947.LOC_Os02g52710.1.

Protein family/group databases

CAZyiGH13. Glycoside Hydrolase Family 13.

Proteomic databases

PaxDbiP17654.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblPlantsiOS02T0765600-01; OS02T0765600-01; OS02G0765600.
GeneIDi4330832.
GrameneiOS02T0765600-01; OS02T0765600-01; OS02G0765600.
KEGGiosa:4330832.

Phylogenomic databases

eggNOGiKOG0471. Eukaryota.
COG0366. LUCA.
HOGENOMiHOG000239525.
InParanoidiP17654.
KOiK01176.
OMAiGEQGYMP.

Enzyme and pathway databases

BRENDAi3.2.1.1. 4460.

Gene expression databases

ExpressionAtlasiP17654. baseline and differential.
GenevisibleiP17654. OS.

Family and domain databases

Gene3Di2.60.40.1180. 1 hit.
3.20.20.80. 1 hit.
InterProiIPR012850. A-amylase_bs_C.
IPR013775. A-amylase_pln.
IPR006046. Alpha_amylase.
IPR015902. Glyco_hydro_13.
IPR006047. Glyco_hydro_13_cat_dom.
IPR013780. Glyco_hydro_b.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
PANTHERiPTHR10357. PTHR10357. 1 hit.
PfamiPF07821. Alpha-amyl_C2. 1 hit.
PF00128. Alpha-amylase. 1 hit.
[Graphical view]
PIRSFiPIRSF001028. Alph-amls_plant. 1 hit.
PRINTSiPR00110. ALPHAAMYLASE.
SMARTiSM00642. Aamy. 1 hit.
SM00810. Alpha-amyl_C2. 1 hit.
[Graphical view]
SUPFAMiSSF51445. SSF51445. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "The alpha-amylase genes in Oryza sativa: characterization of cDNA clones and mRNA expression during seed germination."
    O'Neill S.D., Kumagai M.H., Majumdar A., Huang N., Sutliff T.D., Rodriguez R.L.
    Mol. Gen. Genet. 221:235-244(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
    Strain: cv. M202.
  2. "Classification and characterization of the rice alpha-amylase multigene family."
    Huang N., Sutliff T.D., Litts J.C., Rodriguez R.L.
    Plant Mol. Biol. 14:655-668(1990) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: cv. M202.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: cv. Nipponbare.
  4. Cited for: GENOME REANNOTATION.
    Strain: cv. Nipponbare.

Entry informationi

Entry nameiAMY1_ORYSJ
AccessioniPrimary (citable) accession number: P17654
Secondary accession number(s): Q6Z317
Entry historyi
Integrated into UniProtKB/Swiss-Prot: August 1, 1990
Last sequence update: October 25, 2005
Last modified: May 11, 2016
This is version 130 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

Binds starch not only at the active site, but also via accessory binding sites on the protein surface that are important for efficient binding to starch granules and thereby increase enzyme activity.By similarity

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Glycosyl hydrolases
    Classification of glycosyl hydrolase families and list of entries
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. Oryza sativa (rice)
    Index of Oryza sativa entries and their corresponding gene designations
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.