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P00693 (AMY1_HORVU) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 104. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Alpha-amylase type A isozyme
EC=3.2.1.1
Alternative name(s):
1,4-alpha-D-glucan glucanohydrolase
AMY1
Low pI alpha-amylase
Gene names
Name:AMY1.1
OrganismHordeum vulgare (Barley)
Taxonomic identifier4513 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Pooideae › Triticeae › Hordeum

Protein attributes

Sequence length438 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at protein level

General annotation (Comments)

Catalytic activity

Endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides containing three or more (1->4)-alpha-linked D-glucose units. Ref.2 Ref.5 Ref.7

Cofactor

Binds 3 calcium ions per subunit.

Subunit structure

Monomer.

Subcellular location

Secreted › extracellular space.

Developmental stage

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.

Miscellaneous

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

Mutagenesis experiments indicate that His-117 and His-314 participate in transition state stabilization but not directly in catalysis.

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.

Sequence similarities

Belongs to the glycosyl hydrolase 13 family.

Ontologies

Keywords
   Biological processCarbohydrate metabolism
Germination
   Cellular componentSecreted
   DomainSignal
   LigandCalcium
Metal-binding
   Molecular functionGlycosidase
Hydrolase
   Technical term3D-structure
Gene Ontology (GO)
   Biological processcarbohydrate metabolic process

Inferred from electronic annotation. Source: UniProtKB-KW

   Cellular componentextracellular space

Inferred from electronic annotation. Source: UniProtKB-SubCell

   Molecular functionalpha-amylase activity

Inferred from electronic annotation. Source: EC

calcium ion binding

Inferred from electronic annotation. Source: InterPro

Complete GO annotation...

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Signal peptide1 – 2424
Chain25 – 438414Alpha-amylase type A isozyme
PRO_0000001404

Regions

Region69 – 713Substrate binding
Region76 – 772Substrate binding
Region202 – 2076Substrate binding
Region301 – 3033Substrate binding
Region404 – 4063Substrate binding
Region416 – 4227Substrate binding

Sites

Active site2041Nucleophile Ref.2
Active site2291Proton donor Ref.2
Metal binding1161Calcium 1
Metal binding1331Calcium 2
Metal binding1361Calcium 2; via carbonyl oxygen
Metal binding1381Calcium 2; via carbonyl oxygen
Metal binding1421Calcium 2
Metal binding1521Calcium 3
Metal binding1631Calcium 1
Metal binding1661Calcium 1; via carbonyl oxygen
Metal binding1671Calcium 3
Metal binding1681Calcium 3; via carbonyl oxygen
Metal binding1711Calcium 3; via carbonyl oxygen
Metal binding1731Calcium 1
Metal binding1731Calcium 3
Metal binding2081Calcium 1; via carbonyl oxygen
Binding site2311Substrate
Binding site2331Substrate
Binding site2511Substrate
Binding site2581Substrate
Binding site2951Substrate
Binding site3141Substrate
Binding site3201Substrate
Binding site3991Substrate
Binding site4261Substrate
Site3151Transition state stabilizer

Experimental info

Mutagenesis1171H → N: 20-fold decrease in activity. Ref.2
Mutagenesis1291Y → A: Reduces affinity for starch granules 3-fold. Ref.7
Mutagenesis2041D → A or N: Loss of activity. Ref.2 Ref.5
Mutagenesis2291E → Q: Loss of activity. Ref.2
Mutagenesis3021W → A: Over 10-fold decrease in affinity for starch granules. Abolishes binding of starch granules and reduces activity towards starch granules by 99%; when associated with A-303 and A-404. Ref.3
Mutagenesis3031W → A: Over 10-fold decrease in affinity for starch granules. Abolishes binding of starch granules and reduces activity towards starch granules by 99%; when associated with A-302 and A-404. Ref.2 Ref.3
Mutagenesis3141H → N: 10-fold decrease in activity. Ref.2
Mutagenesis3151D → N: Loss of activity. Ref.2
Mutagenesis4041Y → A: Reduces affinity for starch granules 9-fold and reduces activity by 90%. Abolishes binding of starch granules and reduces activity towards starch granules by 99%; when associated with A-302 and A-303. Ref.3 Ref.6 Ref.7
Mutagenesis4041Y → M: Abolishes binding to cyclodextrin-Sepharose and strongly reduces enzyme activity. Ref.3 Ref.6 Ref.7
Mutagenesis4191H → A: Slightly decreased catalytic activity. Ref.7

Secondary structure

1 ................................................................................. 438
Helix Strand Turn

Details...

Sequences

Sequence LengthMass (Da)Tools
P00693 [UniParc].

Last modified July 21, 1986. Version 1.
Checksum: 2393FDAC51E80F51

FASTA43847,796
        10         20         30         40         50         60 
MGKNGSLCCF SLLLLLLLAG LASGHQVLFQ GFNWESWKQS GGWYNMMMGK VDDIAAAGVT 

        70         80         90        100        110        120 
HVWLPPPSHS VSNEGYMPGR LYDIDASKYG NAAELKSLIG ALHGKGVQAI ADIVINHRCA 

       130        140        150        160        170        180 
DYKDSRGIYC IFEGGTSDGR LDWGPHMICR DDTKYSDGTA NLDTGADFAA APDIDHLNDR 

       190        200        210        220        230        240 
VQRELKEWLL WLKSDLGFDA WRLDFARGYS PEMAKVYIDG TSPSLAVAEV WDNMATGGDG 

       250        260        270        280        290        300 
KPNYDQDAHR QNLVNWVDKV GGAASAGMVF DFTTKGILNA AVEGELWRLI DPQGKAPGVM 

       310        320        330        340        350        360 
GWWPAKAATF VDNHDTGSTQ AMWPFPSDKV MQGYAYILTH PGIPCIFYDH FFNWGFKDQI 

       370        380        390        400        410        420 
AALVAIRKRN GITATSALKI LMHEGDAYVA EIDGKVVVKI GSRYDVGAVI PAGFVTSAHG 

       430 
NDYAVWEKNG AAATLQRS

« Hide

References

[1]"Isolation and sequence analysis of a barley alpha-amylase cDNA clone."
Rogers J.C., Milliman C.
J. Biol. Chem. 258:8169-8174(1983) [PubMed: 6190808] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
Strain: cv. Himalaya.
Tissue: Aleurone.
[2]"Site-directed mutagenesis of histidine 93, aspartic acid 180, glutamic acid 205, histidine 290, and aspartic acid 291 at the active site and tryptophan 279 at the raw starch binding site in barley alpha-amylase 1."
Sogaard M., Kadziola A., Haser R., Svensson B.
J. Biol. Chem. 268:22480-22484(1993) [PubMed: 7901200] [Abstract]
Cited for: MUTAGENESIS OF HIS-117; ASP-204; GLU-229; TRP-303; HIS-314 AND ASP-315, CATALYTIC ACTIVITY, ACTIVE SITE.
[3]"Two secondary carbohydrate binding sites on the surface of barley alpha-amylase 1 have distinct functions and display synergy in hydrolysis of starch granules."
Nielsen M.M., Bozonnet S., Seo E.S., Motyan J.A., Andersen J.M., Dilokpimol A., Abou Hachem M., Gyemant G., Naested H., Kandra L., Sigurskjold B.W., Svensson B.
Biochemistry 48:7686-7697(2009) [PubMed: 19606835] [Abstract]
Cited for: MUTAGENESIS OF TRP-302; TRP-303 AND TYR-404.
[4]"The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs."
Robert X., Haser R., Gottschalk T.E., Ratajczak F., Driguez H., Svensson B., Aghajari N.
Structure 11:973-984(2003) [PubMed: 12906828] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-428 IN COMPLEX WITH CALCIUM IONS.
[5]"Oligosaccharide binding to barley alpha-amylase 1."
Robert X., Haser R., Mori H., Svensson B., Aghajari N.
J. Biol. Chem. 280:32968-32978(2005) [PubMed: 16030022] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) OF 25-429 IN COMPLEXES WITH CALCIUM IONS; ACARBOSE AND MALTOHEPTAOSE, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-204.
[6]"The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity."
Bozonnet S., Jensen M.T., Nielsen M.M., Aghajari N., Jensen M.H., Kramhoeft B., Willemoes M., Tranier S., Haser R., Svensson B.
FEBS J. 274:5055-5067(2007) [PubMed: 17803687] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.70 ANGSTROMS) OF 25-429 IN COMPLEX WITH CALCIUM IONS AND ACARBOSE, MUTAGENESIS OF TYR-404.
[7]"Multi-site substrate binding and interplay in barley alpha-amylase 1."
Nielsen M.M., Seo E.S., Bozonnet S., Aghajari N., Robert X., Haser R., Svensson B.
FEBS Lett. 582:2567-2571(2008) [PubMed: 18588886] [Abstract]
Cited for: X-RAY CRYSTALLOGRAPHY (1.95 ANGSTROMS) IN COMPLEXES WITH CALCIUM IONS AND GLUCOSE, CATALYTIC ACTIVITY, MUTAGENESIS OF TYR-129; TYR-404 AND HIS-419.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		J01236 mRNA. Translation: AAA32929.1.
PIRALBH. A00846.
UniGeneHv.68.

3D structure databases

PDBe
RCSB PDB
PDBj
EntryMethodResolution (Å)ChainPositionsPDBsum
1HT6X-ray1.50A25-429[»]
1P6WX-ray2.00A25-429[»]
1RP8X-ray2.00A25-429[»]
1RP9X-ray2.00A25-429[»]
1RPKX-ray2.00A25-429[»]
2QPSX-ray2.20A25-429[»]
2QPUX-ray1.70A/B/C25-429[»]
3BSGX-ray1.95A25-438[»]
3BSHX-ray3.00A25-438[»]
ProteinModelPortalP00693.
SMRP00693. Positions 25-428.
ModBaseSearch...

Protein family/group databases

CAZyGH13. Glycoside Hydrolase Family 13.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Organism-specific databases

GrameneP00693.

Enzyme and pathway databases

BRENDA3.2.1.1. 2687.

Gene expression databases

GenevestigatorP00693.

Family and domain databases

InterProIPR012850. A-amylase_bs_C.
IPR013775. A-amylase_pln.
IPR015902. Alpha_amylase.
IPR006046. Glyco_hydro_13.
IPR013780. Glyco_hydro_13_b.
IPR006047. Glyco_hydro_13_cat_dom.
IPR006589. Glyco_hydro_13_sub_cat_dom.
IPR013781. Glyco_hydro_subgr_catalytic.
IPR017853. Glycoside_hydrolase_SF.
[Graphical view]
Gene3DG3DSA:2.60.40.1180. Glyco_hydro_13_b. 1 hit.
G3DSA:3.20.20.80. Glyco_hydro_cat. 1 hit.
PANTHERPTHR10357. Alpha_amylase. 1 hit.
PfamPF07821. Alpha-amyl_C2. 1 hit.
PF00128. Alpha-amylase. 1 hit.
[Graphical view]
PIRSFPIRSF001028. Alph-amls_plant. 1 hit.
PRINTSPR00110. ALPHAAMYLASE.
SMARTSM00642. Aamy. 1 hit.
SM00810. Alpha-amyl_C2. 1 hit.
[Graphical view]
SUPFAMSSF51445. Glyco_hydro_cat. 1 hit.
ProtoNetSearch...

Entry information

Entry nameAMY1_HORVU
AccessionPrimary (citable) accession number: P00693
Entry history
Integrated into UniProtKB/Swiss-Prot: July 21, 1986
Last sequence update: July 21, 1986
Last modified: December 14, 2011
This is version 104 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programPlant Protein Annotation Program

Relevant documents

Glycosyl hydrolases

Classification of glycosyl hydrolase families and list of entries

PDB cross-references

Index of Protein Data Bank (PDB) cross-references

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents