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P27933 (AMY3D_ORYSJ) Reviewed, UniProtKB/Swiss-Prot

Last modified December 14, 2011. Version 91. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (3) | Third-party data text xml rdf/xml gff fasta
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Names and origin

Protein namesRecommended name:
Alpha-amylase isozyme 3D
EC=3.2.1.1
Alternative name(s):
1,4-alpha-D-glucan glucanohydrolase
Gene names
Name:AMY1.3
Synonyms:AMY3D
Ordered Locus Names:Os08g0473900, LOC_Os08g36910
ORF Names:P0013B04.36-1, P0451G12.5-1
OrganismOryza sativa subsp. japonica (Rice)
Taxonomic identifier39947 [NCBI]
Taxonomic lineageEukaryota › Viridiplantae › Streptophyta › Embryophyta › Tracheophyta › Spermatophyta › Magnoliophyta › Liliopsida › Poales › Poaceae › BEP clade › Ehrhartoideae › Oryzeae › Oryza

Protein attributes

Sequence length436 AA.
Sequence statusComplete.
Sequence processingThe displayed sequence is further processed into a mature form.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

Important for breakdown of endosperm starch during germination.

Catalytic activity

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

Cofactor

Binds 3 calcium ions per subunit By similarity.

Subunit structure

Monomer.

Tissue specificity

Is expressed in all tissues, except in immature seeds. Is the most abundant alpha-amylase isozyme in callus.

Developmental stage

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.

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.

Sequence similarities

Belongs to the glycosyl hydrolase 13 family.

Ontologies

Keywords
   Biological processCarbohydrate metabolism
   DomainSignal
   LigandCalcium
Metal-binding
   Molecular functionGlycosidase
Hydrolase
Gene Ontology (GO)
   Biological processstarch catabolic process

Inferred from expression pattern. Source: Gramene

sucrose catabolic process

Inferred from expression pattern. Source: Gramene

   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 – 2525 Potential
Chain26 – 436411Alpha-amylase isozyme 3D
PRO_0000001415

Regions

Region76 – 772Substrate binding By similarity
Region202 – 2076Substrate binding By similarity
Region298 – 3003Substrate binding By similarity
Region401 – 4033Substrate binding By similarity

Sites

Active site2041Nucleophile By similarity
Active site2291Proton donor By similarity
Metal binding1161Calcium 1 By similarity
Metal binding1331Calcium 2 By similarity
Metal binding1361Calcium 2; via carbonyl oxygen By similarity
Metal binding1381Calcium 2; via carbonyl oxygen By similarity
Metal binding1421Calcium 2 By similarity
Metal binding1521Calcium 3 By similarity
Metal binding1631Calcium 1 By similarity
Metal binding1681Calcium 3; via carbonyl oxygen By similarity
Metal binding1711Calcium 3; via carbonyl oxygen By similarity
Metal binding1731Calcium 1 By similarity
Metal binding1731Calcium 3 By similarity
Metal binding2081Calcium 1; via carbonyl oxygen By similarity
Binding site2311Substrate By similarity
Binding site2331Substrate By similarity
Binding site2511Substrate By similarity
Binding site2921Substrate By similarity
Binding site3111Substrate By similarity
Binding site3171Substrate By similarity
Binding site3961Substrate By similarity
Binding site4231Substrate By similarity
Site3121Transition state stabilizer By similarity

Experimental info

Sequence conflict73 – 742PQ → R in AAA33886. Ref.2
Sequence conflict1371P → R in AAA33886. Ref.2
Sequence conflict1381Missing in AAA33895. Ref.1
Sequence conflict1381Missing in AAA33886. Ref.2
Sequence conflict2941A → P in AAA33895. Ref.1
Sequence conflict2941A → P in AAA33886. Ref.2

Sequences

Sequence LengthMass (Da)Tools
P27933 [UniParc].

Last modified October 25, 2005. Version 2.
Checksum: D353346D13D3DC93

FASTA43648,000
        10         20         30         40         50         60 
MKNTSSLCLL LLVVLCSLTC NSGQAQVLFQ GFNWESWKQQ GGWYNMLKGQ VDDIAKAGVT 

        70         80         90        100        110        120 
HVWLPPPSHS VAPQGYMPGR LYDLDASKYG TAAELKSLIA AFHGKGVQCV ADVVINHRCA 

       130        140        150        160        170        180 
EKKDARGVYC VFEGGTPDDR LDWGPGMICS DDTQYSDGTG HRDTGEGFGA APDIDHLNPR 

       190        200        210        220        230        240 
VQRELTDWLN WLKSDVGFDG WRLDFAKGYS TDIAKMYVES CKPGFVVAEI WNSLSYNGDG 

       250        260        270        280        290        300 
KPAANQDQGR QELVNWVNAV GGPAMTFDFT TKGLLQAGVQ GELWRLRDGN GKAAGMIGWL 

       310        320        330        340        350        360 
PEKAVTFVDN HDTGSTQKLW PFPSDKVMQG YAYILTHPGV PCIFYDHMFD WNLKQEITAL 

       370        380        390        400        410        420 
AAIRERNGIN AGSKLRIVVA DADAYVAVVD EKVMVKIGTR YDVGNAVPSD FHQTVHGKDY 

       430 
SVWEKGSLRV PAGRHL

« Hide

References

« Hide 'large scale' references
[1]"Structural organization and differential expression of rice alpha-amylase genes."
Huang N., Koizumi N., Reinl S.J., Rodriguez R.L.
Nucleic Acids Res. 18:7007-7014(1990) [PubMed: 2263460] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
Strain: cv. M202.
Tissue: Etiolated leaf.
[2]"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: 2370848] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"The map-based sequence of the rice genome."
International rice genome sequencing project (IRGSP)
Nature 436:793-800(2005) [PubMed: 16100779] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: cv. Nipponbare.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		M59351 Genomic DNA. Translation: AAA33895.1.
M24287 mRNA. Translation: AAA33886.1.
AP004399 Genomic DNA. Translation: BAD09335.1.
AP004457 Genomic DNA. Translation: BAD09375.1.
PIRS12625.

3D structure databases

ProteinModelPortalP27933.
SMRP27933. Positions 26-425.
ModBaseSearch...

Protein family/group databases

CAZyGH13. Glycoside Hydrolase Family 13.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Organism-specific databases

GrameneP27933.

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 nameAMY3D_ORYSJ
AccessionPrimary (citable) accession number: P27933
Secondary accession number(s): Q6ZDD5
Entry history
Integrated into UniProtKB/Swiss-Prot: August 1, 1992
Last sequence update: October 25, 2005
Last modified: December 14, 2011
This is version 91 of the entry and version 2 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

Oryza sativa (rice)

Index of Oryza sativa entries and their corresponding gene designations

SIMILARITY comments

Index of protein domains and families

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