Native structure of chimaeric amylase from B. amyloliquefaciens and B. licheniformis at 1.7A

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.133 

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Structural Analysis of a Chimeric Bacterial Alpha-Amylase. High Resolution Analysis of Native and Ligand Complexes

Brzozowski, A.M.Lawson, D.M.Turkenburg, J.P.Bisgaard-Frantzen, H.Svendsen, A.Borchert, T.V.Dauter, Z.Wilson, K.S.Davies, G.J.

(2000) Biochemistry 39: 9099

  • DOI: https://doi.org/10.1021/bi0000317
  • Primary Citation of Related Structures:  
    1E3X, 1E3Z, 1E40, 1E43

  • PubMed Abstract: 

    Several chimeric alpha-amylases genes were constructed by an in vivo recombination technique from the Bacillus amyloliquefaciens and Bacillus licheniformis genes. One of the fusion amylases (hereafter BA2), consisting of residues 1-300 from B. amyloliquefaciens and 301-483 from B. licheniformis, has been extensively studied by X-ray crystallography at resolutions between 2.2 and 1.7 A. The 3-dimensional structure of the native enzyme was solved by multiple isomorphous replacement, and refined at a resolution of 1.7 A. It consists of 483 amino acids, organized similarly to the known B. lichiniformis alpha-amylase structure [Machius et al. (1995) J. Mol. Biol. 246, 545-559], but features 4 bound calcium ions. Two of these form part of a linear cluster of three ions, the central ion being attributed to sodium. This cluster lies at the junction of the A and B domains with one calcium of the cluster structurally equivalent to the major Ca(2+) binding site of fungal alpha-amylases. The third calcium ion is found at the interface of the A and C domains. BA2 contains a fourth calcium site, not observed in the B. licheniformis alpha-amylase structure. It is found on the C domain where it bridges the two beta-sheets. Three acid residues (Glu261, Asp328, and Asp231) form an active site similar to that seen in other amylases. In the presence of TRIS buffer, a single molecule of TRIS occupies the -1 subsite of the enzyme where it is coordinated by the three active-center carboxylates. Kinetic data reveal that BA2 displays properties intermediate to those of its parents. Data for crystals soaked in maltooligosaccharides reveal the presence of a maltotriose binding site on the N-terminal face of the (beta/alpha)(8) barrel of the molecule, not previously described for any alpha-amylase structure, the biological function of which is unclear. Data for a complex soaked with the tetrasaccharide inhibitor acarbose, at 1.9 A, reveal a decasaccharide moiety, spanning the -7 to +3 subsites of the enzyme. The unambiguous presence of three unsaturated rings in the (2)H(3) half-chair/(2)E envelope conformation, adjacent to three 6-deoxypyranose units, clearly demonstrates synthesis of this acarbose-derived decasaccharide by a two-step transglycosylation mechanism.

  • Organizational Affiliation

    Department of Chemistry, Structural Biology Laboratory, University of York, Heslington, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ALPHA-AMYLASE483Bacillus amyloliquefaciensMutation(s): 0 
Find proteins for P00692 (Bacillus amyloliquefaciens)
Explore P00692 
Go to UniProtKB:  P00692
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00692
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.185 
  • R-Value Work: 0.133 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.2α = 90
b = 76.1β = 90
c = 236.5γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2001-06-21
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-05-08
    Changes: Advisory, Data collection, Experimental preparation, Other
  • Version 1.4: 2023-12-13
    Changes: Advisory, Data collection, Database references, Derived calculations, Other, Refinement description