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P04063

- AMY2_HORVU

UniProt

P04063 - AMY2_HORVU

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Protein
Alpha-amylase type B isozyme
Gene
AMY1.2
Organism
Hordeum vulgare (Barley)
Status
Reviewed - Annotation score: 5 out of 5 - Experimental evidence at protein leveli

Functioni

Catalytic activityi

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

Cofactori

Binds 3 calcium ions per subunit.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi115 – 1151Calcium 1
Metal bindingi132 – 1321Calcium 2
Metal bindingi135 – 1351Calcium 2; via carbonyl oxygen
Metal bindingi137 – 1371Calcium 2; via carbonyl oxygen
Metal bindingi141 – 1411Calcium 2
Metal bindingi151 – 1511Calcium 3
Metal bindingi162 – 1621Calcium 1
Metal bindingi165 – 1651Calcium 1; via carbonyl oxygen
Metal bindingi166 – 1661Calcium 3
Metal bindingi167 – 1671Calcium 3; via carbonyl oxygen
Metal bindingi170 – 1701Calcium 3; via carbonyl oxygen
Metal bindingi172 – 1721Calcium 1
Metal bindingi172 – 1721Calcium 3
Active sitei203 – 2031Nucleophile1 Publication
Metal bindingi207 – 2071Calcium 1; via carbonyl oxygen
Active sitei228 – 2281Proton donor1 Publication
Binding sitei230 – 2301Substrate
Binding sitei232 – 2321Substrate
Binding sitei250 – 2501Substrate
Binding sitei257 – 2571Substrate
Binding sitei293 – 2931Substrate By similarity
Binding sitei312 – 3121Substrate
Sitei313 – 3131Transition state stabilizer
Binding sitei318 – 3181Substrate By similarity
Binding sitei397 – 3971Substrate By similarity
Binding sitei424 – 4241Substrate By similarity

GO - Molecular functioni

  1. alpha-amylase activity Source: UniProtKB-EC
  2. calcium ion binding Source: InterPro

GO - Biological processi

  1. carbohydrate metabolic process Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Glycosidase, Hydrolase

Keywords - Biological processi

Carbohydrate metabolism, Germination

Keywords - Ligandi

Calcium, Metal-binding

Enzyme and pathway databases

BRENDAi3.2.1.1. 2687.

Protein family/group databases

CAZyiGH13. Glycoside Hydrolase Family 13.

Names & Taxonomyi

Protein namesi
Recommended name:
Alpha-amylase type B isozyme (EC:3.2.1.1)
Alternative name(s):
1,4-alpha-D-glucan glucanohydrolase
AMY2-2
High pI alpha-amylase
Gene namesi
Name:AMY1.2
OrganismiHordeum vulgare (Barley)
Taxonomic identifieri4513 [NCBI]
Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBEP cladePooideaeTriticeaeHordeum

Organism-specific databases

GrameneiP04063.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Signal peptidei1 – 2424
Add
BLAST
Chaini25 – 427403Alpha-amylase type B isozyme
PRO_0000001405Add
BLAST

Expressioni

Developmental stagei

Production of alpha-amylase is hormonally regulated. Germinating embryos produce the hormone gibberellic acid, which within 10 hours stimulates the aleurone cells covering the endosperm of the seed to produce alpha-amylase. The enzyme then degrades the starch within the endosperm for use by the developing plant embryo.

Inductioni

Type B isozyme mRNA is undetectable in unstimulated cells and increases a hundred-fold after stimulation with gibberellic acid.

Gene expression databases

GenevestigatoriP04063.

Interactioni

Subunit structurei

Monomer.

Protein-protein interaction databases

DIPiDIP-6097N.

Structurei

Secondary structure

Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 293
Helixi35 – 373
Helixi42 – 476
Helixi50 – 567
Beta strandi60 – 634
Beta strandi69 – 713
Beta strandi74 – 774
Helixi83 – 853
Helixi91 – 10414
Beta strandi107 – 1126
Beta strandi120 – 1223
Beta strandi128 – 1303
Beta strandi134 – 1385
Helixi144 – 1463
Turni152 – 1543
Beta strandi163 – 1653
Beta strandi168 – 1703
Helixi178 – 19316
Beta strandi199 – 2024
Helixi205 – 2073
Helixi210 – 22011
Beta strandi223 – 2275
Beta strandi239 – 2413
Helixi246 – 26015
Beta strandi263 – 2686
Helixi270 – 27910
Turni280 – 2823
Helixi284 – 2874
Helixi297 – 2993
Helixi302 – 3043
Beta strandi305 – 3095
Turni312 – 3143
Turni316 – 3183
Helixi325 – 3273
Helixi328 – 33710
Beta strandi338 – 3458
Helixi346 – 3505
Helixi355 – 36713
Beta strandi376 – 3827
Beta strandi385 – 3906
Turni391 – 3933
Beta strandi394 – 4007
Helixi405 – 4073
Beta strandi410 – 4189
Beta strandi421 – 4266

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1AMYX-ray2.80A25-427[»]
1AVAX-ray1.90A/B25-427[»]
1BG9X-ray2.80A25-427[»]
ProteinModelPortaliP04063.
SMRiP04063. Positions 25-427.

Miscellaneous databases

EvolutionaryTraceiP04063.

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni75 – 762Substrate binding By similarity
Regioni201 – 2066Substrate binding
Regioni299 – 3013Substrate binding
Regioni402 – 4043Substrate binding By similarity

Sequence similaritiesi

Keywords - Domaini

Signal

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.
IPR013780. Glyco_hydro_13_b.
IPR006047. Glyco_hydro_13_cat_dom.
IPR006589. Glyco_hydro_13_sub_cat_dom.
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.

P04063-1 [UniParc]FASTAAdd to Basket

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MANKHLSLSL FLVLLGLSAS LASGQVLFQG FNWESWKHNG GWYNFLMGKV    50
DDIAAAGITH VWLPPASQSV AEQGYMPGRL YDLDASKYGN KAQLKSLIGA 100
LHGKGVKAIA DIVINHRTAE HKDGRGIYCI FEGGTPDARL DWGPHMICRD 150
DRPYADGTGN PDTGADFGAA PDIDHLNLRV QKELVEWLNW LKADIGFDGW 200
RFDFAKGYSA DVAKIYIDRS EPSFAVAEIW TSLAYGGDGK PNLNQDQHRQ 250
ELVNWVDKVG GKGPATTFDF TTKGILNVAV EGELWRLRGT DGKAPGMIGW 300
WPAKAVTFVD NHDTGSTQHM WPFPSDRVMQ GYAYILTHPG TPCIFYDHFF 350
DWGLKEEIDR LVSVRTRHGI HNESKLQIIE ADADLYLAEI DGKVIVKLGP 400
RYDVGNLIPG GFKVAAHGND YAVWEKI 427
Length:427
Mass (Da):47,356
Last modified:July 15, 1998 - v3
Checksum:i957C0B16621BF748
GO

Sequence conflict

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti134 – 1341G → D in CAA33298. 1 Publication
Sequence conflicti425 – 4251E → Q in CAA33298. 1 Publication

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X15226 Genomic DNA. Translation: CAA33298.1.
K02637 Genomic DNA. Translation: AAA98790.1.
PIRiA31960. ALBHB.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
X15226 Genomic DNA. Translation: CAA33298.1 .
K02637 Genomic DNA. Translation: AAA98790.1 .
PIRi A31960. ALBHB.

3D structure databases

Select the link destinations:
PDBe
RCSB PDB
PDBj
Links Updated
Entry Method Resolution (Å) Chain Positions PDBsum
1AMY X-ray 2.80 A 25-427 [» ]
1AVA X-ray 1.90 A/B 25-427 [» ]
1BG9 X-ray 2.80 A 25-427 [» ]
ProteinModelPortali P04063.
SMRi P04063. Positions 25-427.
ModBasei Search...
MobiDBi Search...

Protein-protein interaction databases

DIPi DIP-6097N.

Protein family/group databases

CAZyi GH13. Glycoside Hydrolase Family 13.

Protocols and materials databases

Structural Biology Knowledgebase Search...

Organism-specific databases

Gramenei P04063.

Enzyme and pathway databases

BRENDAi 3.2.1.1. 2687.

Miscellaneous databases

EvolutionaryTracei P04063.

Gene expression databases

Genevestigatori P04063.

Family and domain databases

Gene3Di 2.60.40.1180. 1 hit.
3.20.20.80. 1 hit.
InterProi IPR012850. A-amylase_bs_C.
IPR013775. A-amylase_pln.
IPR006046. Alpha_amylase.
IPR015902. Glyco_hydro_13.
IPR013780. Glyco_hydro_13_b.
IPR006047. Glyco_hydro_13_cat_dom.
IPR006589. Glyco_hydro_13_sub_cat_dom.
IPR013781. Glyco_hydro_catalytic_dom.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view ]
PANTHERi PTHR10357. PTHR10357. 1 hit.
Pfami PF07821. Alpha-amyl_C2. 1 hit.
PF00128. Alpha-amylase. 1 hit.
[Graphical view ]
PIRSFi PIRSF001028. Alph-amls_plant. 1 hit.
PRINTSi PR00110. ALPHAAMYLASE.
SMARTi SM00642. Aamy. 1 hit.
SM00810. Alpha-amyl_C2. 1 hit.
[Graphical view ]
SUPFAMi SSF51445. SSF51445. 1 hit.
ProtoNeti Search...

Publicationsi

  1. "Nucleotide and predicted amino acid sequences of two different genes for high-pI alpha-amylases from barley."
    Rahmatullah R.J., Huang J.K., Clark K.L., Reeck G.R., Chandra G.R., Muthukrishnan S.
    Plant Mol. Biol. 12:119-121(1989)
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "Two barley alpha-amylase gene families are regulated differently in aleurone cells."
    Rogers J.C.
    J. Biol. Chem. 260:3731-3738(1985) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  3. "Crystal and molecular structure of barley alpha-amylase."
    Kadziola A., Abe J.-I., Svensson B., Haser R.
    J. Mol. Biol. 239:104-121(1994) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) IN COMPLEX WITH CALCIUM IONS.
  4. "Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis."
    Kadziola A., Sogaard M., Svensson B., Haser R.
    J. Mol. Biol. 278:205-217(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS) OF 25-427 IN COMPLEX WITH CALCIUM IONS AND ACARBOSE, ACTIVE SITE.
  5. "Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9-A resolution."
    Vallee F., Kadziola A., Bourne Y., Juy M., Rodenburg K.W., Svensson B., Haser R.
    Structure 6:649-659(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH BASI AND CALCIUM IONS.
    Strain: cv. Menuet.

Entry informationi

Entry nameiAMY2_HORVU
AccessioniPrimary (citable) accession number: P04063
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1986
Last sequence update: July 15, 1998
Last modified: October 16, 2013
This is version 107 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Miscellaneousi

Miscellaneous

There are at least 4 types of alpha-amylase in barley.
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.

Keywords - Technical termi

3D-structure

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. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

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