PDBsum entry 2gvy

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protein ligands metals Protein-protein interface(s) links
Hydrolase PDB id
Protein chains
476 a.a. *
_CA ×2
Waters ×751
* Residue conservation analysis
PDB id:
Name: Hydrolase
Title: Monoclinic crystal form of aspergillus niger alpha-amylase i with maltose at 1.8 a resolution
Structure: Alpha-amylase a. Chain: a, b. Synonym: taka-amylase a, taa, 1,4- alpha-d-glucan glucanohy engineered: yes
Source: Aspergillus oryzae. Organism_taxid: 5062. Gene: amy1. Expressed in: aspergillus oryzae. Expression_system_taxid: 5062
1.80Å     R-factor:   0.165     R-free:   0.210
Authors: A.Vujicic-Zagar,B.W.Dijkstra
Key ref:
A.Vujicić-Zagar and B.W.Dijkstra (2006). Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution. Acta Crystallograph Sect F Struct Biol Cryst Commun, 62, 716-721. PubMed id: 16880540 DOI: 10.1107/S1744309106024729
03-May-06     Release date:   15-Aug-06    
Go to PROCHECK summary

Protein chains
Pfam   ArchSchema ?
P0C1B3  (AMYA1_ASPOR) -  Alpha-amylase A type-1/2
499 a.a.
476 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.  - Alpha-amylase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Endohydrolysis of 1,4-alpha-glucosidic linkages in oligosaccharides and polysaccharides.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cellular_component   6 terms 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     7 terms  


DOI no: 10.1107/S1744309106024729 Acta Crystallograph Sect F Struct Biol Cryst Commun 62:716-721 (2006)
PubMed id: 16880540  
Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 angstroms resolution.
A.Vujicić-Zagar, B.W.Dijkstra.
Aspergillus niger alpha-amylase catalyses the hydrolysis of alpha-1,4-glucosidic bonds in starch. It shows 100% sequence identity to the A. oryzae homologue (also called TAKA-amylase), three crystal structures of which have been published to date. Two of them belong to the orthorhombic space group P2(1)2(1)2(1) with one molecule per asymmetric unit and one belongs to the monoclinic space group P2(1) with three molecules per asymmetric unit. Here, the purification, crystallization and structure determination of A. niger alpha-amylase crystallized in the monoclinic space group P2(1) with two molecules per asymmetric unit in complex with maltose at 1.8 angstroms resolution is reported. Furthermore, a novel 1.6 angstroms resolution orthorhombic crystal form (space group P2(1)2(1)2) of the native enzyme is presented. Four maltose molecules are observed in the maltose-alpha-amylase complex. Three of these occupy active-site subsites -2 and -1, +1 and +2 and the hitherto unobserved subsites +4 (Asp233, Gly234) and +5 (Asp235). The fourth maltose molecule binds at the distant binding sites d1 (Tyr382) and d2 (Trp385), also previously unobserved. Furthermore, it is shown that the active-site groove permits different binding modes of sugar units at subsites +1 and +2. This flexibility of the active-site cleft close to the catalytic centre might be needed for a productive binding of substrate chains and/or release of products.
  Selected figure(s)  
Figure 1.
Figure 1 Maltose versus acarbose binding in A. niger -amylase. (a) Schematic presentation of the acarbose-derived hexasaccharide bound in the TAKA-amylase structure (PDB code 7taa ; Brzozowski & Davies, 1997[Brzozowski, A. M. & Davies, G. J. (1997). Biochemistry, 36, 10837-10845.]) with the inhibitor acarbose bound at subsites -1 to +3. According to Brzozowski & Davies (1997[Brzozowski, A. M. & Davies, G. J. (1997). Biochemistry, 36, 10837-10845.]), the maltosyl moiety of the hexasaccharide bound at the -3 and -2 subsites resulted from overlapping binding modes of acarbose. Beneath the hexasaccharide presentation, three maltose molecules M1, M2 and M3, which occupy subsites -2 and -1, +1 and +2, and +4 and +5, respectively, are depicted. (b) Molecular-surface representation of molecule A with bound maltose molecules M1, M2, M3 and M4 shown in yellow stick representation. The three domains A, B and C are coloured green, red and yellow, respectively. The above-mentioned hexasaccharide molecule, shown in white stick representation, is superimposed on the present structure (using the program XtalView; McRee, 1992[McRee, D. E. (1992). J. Mol. Graph. 10, 44-46.]). Substrate-binding subsites are numbered from -3 to +5.
Figure 2.
Figure 2 C^ -trace of superimposed P2[1] and P2[1]2[1]2 crystal structures of A. niger -amylase coloured green and orange, respectively. The glycosylated side chain of Asn197 is shown in stick representation. Structure superposition was carried out using the program XtalView (McRee, 1992[McRee, D. E. (1992). J. Mol. Graph. 10, 44-46.]).
  The above figures are reprinted by permission from the IUCr: Acta Crystallograph Sect F Struct Biol Cryst Commun (2006, 62, 716-721) copyright 2006.  
  Figures were selected by the author.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18071262 S.Kato, A.Shimizu-Ibuka, K.Mura, A.Takeuchi, C.Tokue, and S.Arai (2007).
Molecular cloning and characterization of an alpha-amylase from Pichia burtonii 15-1.
  Biosci Biotechnol Biochem, 71, 3007-3013.  
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