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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

Ca2+Note: Binds 3 Ca(2+) 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 – 2931SubstrateBy similarity
Binding sitei312 – 3121Substrate
Sitei313 – 3131Transition state stabilizer
Binding sitei318 – 3181SubstrateBy similarity
Binding sitei397 – 3971SubstrateBy similarity
Binding sitei424 – 4241SubstrateBy 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 – 2424Add
BLAST
Chaini25 – 427403Alpha-amylase type B isozymePRO_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.2 Publications

Protein-protein interaction databases

DIPiDIP-6097N.

Structurei

Secondary structure

1
427
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi27 – 293Combined sources
Helixi35 – 373Combined sources
Helixi42 – 476Combined sources
Helixi50 – 567Combined sources
Beta strandi60 – 634Combined sources
Beta strandi69 – 713Combined sources
Beta strandi74 – 774Combined sources
Helixi83 – 853Combined sources
Helixi91 – 10414Combined sources
Beta strandi107 – 1126Combined sources
Beta strandi120 – 1223Combined sources
Beta strandi128 – 1303Combined sources
Beta strandi134 – 1385Combined sources
Helixi144 – 1463Combined sources
Turni152 – 1543Combined sources
Beta strandi163 – 1653Combined sources
Beta strandi168 – 1703Combined sources
Helixi178 – 19316Combined sources
Beta strandi199 – 2024Combined sources
Helixi205 – 2073Combined sources
Helixi210 – 22011Combined sources
Beta strandi223 – 2275Combined sources
Beta strandi239 – 2413Combined sources
Helixi246 – 26015Combined sources
Beta strandi263 – 2686Combined sources
Helixi270 – 27910Combined sources
Turni280 – 2823Combined sources
Helixi284 – 2874Combined sources
Helixi297 – 2993Combined sources
Helixi302 – 3043Combined sources
Beta strandi305 – 3095Combined sources
Turni312 – 3143Combined sources
Turni316 – 3183Combined sources
Helixi325 – 3273Combined sources
Helixi328 – 33710Combined sources
Beta strandi338 – 3458Combined sources
Helixi346 – 3505Combined sources
Helixi355 – 36713Combined sources
Beta strandi376 – 3827Combined sources
Beta strandi385 – 3906Combined sources
Turni391 – 3933Combined sources
Beta strandi394 – 4007Combined sources
Helixi405 – 4073Combined sources
Beta strandi410 – 4189Combined sources
Beta strandi421 – 4266Combined sources

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiP04063.

Family & Domainsi

Region

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

Sequence similaritiesi

Belongs to the glycosyl hydrolase 13 family.Curated

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

« Hide

        10         20         30         40         50
MANKHLSLSL FLVLLGLSAS LASGQVLFQG FNWESWKHNG GWYNFLMGKV
60 70 80 90 100
DDIAAAGITH VWLPPASQSV AEQGYMPGRL YDLDASKYGN KAQLKSLIGA
110 120 130 140 150
LHGKGVKAIA DIVINHRTAE HKDGRGIYCI FEGGTPDARL DWGPHMICRD
160 170 180 190 200
DRPYADGTGN PDTGADFGAA PDIDHLNLRV QKELVEWLNW LKADIGFDGW
210 220 230 240 250
RFDFAKGYSA DVAKIYIDRS EPSFAVAEIW TSLAYGGDGK PNLNQDQHRQ
260 270 280 290 300
ELVNWVDKVG GKGPATTFDF TTKGILNVAV EGELWRLRGT DGKAPGMIGW
310 320 330 340 350
WPAKAVTFVD NHDTGSTQHM WPFPSDRVMQ GYAYILTHPG TPCIFYDHFF
360 370 380 390 400
DWGLKEEIDR LVSVRTRHGI HNESKLQIIE ADADLYLAEI DGKVIVKLGP
410 420
RYDVGNLIPG GFKVAAHGND YAVWEKI
Length:427
Mass (Da):47,356
Last modified:July 15, 1998 - v3
Checksum:i957C0B16621BF748
GO

Experimental Info

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

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15226 Genomic DNA. Translation: CAA33298.1.
K02637 Genomic DNA. Translation: AAA98790.1.
PIRiA31960. ALBHB.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X15226 Genomic DNA. Translation: CAA33298.1 .
K02637 Genomic DNA. Translation: AAA98790.1 .
PIRi A31960. ALBHB.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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: November 26, 2014
This is version 109 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