1amy
From Proteopedia
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CRYSTAL AND MOLECULAR STRUCTURE OF BARLEY ALPHA-AMYLASE
Overview
The three-dimensional structure of barley malt alpha-amylase (isoform, AMY2-2) was determined by multiple isomorphous replacement using three, heavy-atom derivatives and solvent flattening. The model was refined using, a combination of simulated annealing and conventional restrained, least-squares crystallographic refinement to an R-factor of 0.153 based on, 18,303 independent reflections with F(o) > sigma(F(o)) between 10 and 2.8, A resolution, with root-mean-square deviations of 0.016 A and 3.3 degrees, from ideal bond lengths and bond angles, respectively. The final model, consists of 403 amino acid residues, three calcium ions and 153 water, molecules. The polypeptide chain folds into three domains: a central, domain forming a (beta alpha)8-barrel of 286 residues, with a protruding, irregular structured loop domain of 64 residues (domain B) connecting, strand beta 3 and helix alpha 3 of the barrel, and a C-terminal domain of, 53 residues forming a five stranded anti-parallel beta-sheet. Unlike the, previously known alpha-amylase structures, AMY2-2 contains three Ca2+, binding sites co-ordinated by seven or eight oxygen atoms from carboxylate, groups, main-chain carbonyl atoms and water molecules, all calcium ions, being bound to domain B and therefore essential for the structural, integrity of that domain. Two of the Ca2+ sites are located only 7.0 A, apart with one Asp residue serving as ligand for both. One Ca2+ site, located at about 20 A from the other two was found to be exchangeable with, Eu3+. By homology with other alpha-amylases, some important active site, residues are identified as Asp179, Glu204 and Asp289, and are situated at, the C-terminal end of the central beta-barrel. A starch granule binding, site, previously identified as Trp276 and Trp277, is situated on, alpha-helix 6 in the central (beta alpha)8-barrel, at the surface of the, enzyme. This binding site region is associated with a considerable, disruption of the (beta alpha)8-barrel 8-fold symmetry.
About this Structure
1AMY is a Single protein structure of sequence from Hordeum vulgare with CA as ligand. Active as Alpha-amylase, with EC number 3.2.1.1 Full crystallographic information is available from OCA.
Reference
Crystal and molecular structure of barley alpha-amylase., Kadziola A, Abe J, Svensson B, Haser R, J Mol Biol. 1994 May 27;239(1):104-21. PMID:8196040
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