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P04063

- AMY2_HORVU

UniProt

P04063 - AMY2_HORVU

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
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    • History
      Entry version 108 (01 Oct 2014)
      Sequence version 3 (15 Jul 1998)
      Previous versions | rss
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    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 – 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

    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 – 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.
    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

    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

    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:
    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 1, 2014
    This is version 108 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