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PDBsum entry 1amy

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Hydrolase (o-glycosyl) PDB id
1amy
Jmol
Contents
Protein chain
403 a.a.
Metals
_CA ×3
Waters ×152

References listed in PDB file
Key reference
Title Crystal and molecular structure of barley alpha-Amylase.
Authors A.Kadziola, J.Abe, B.Svensson, R.Haser.
Ref. J Mol Biol, 1994, 239, 104-121.
PubMed id 8196040
Abstract
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.
Secondary reference #1
Title Characterization, Crystallization and preliminary X-Ray crystallographic analysis of the complex between barley alpha-Amylase and the bifunctional alpha-Amylase/subtilisin inhibitor from barley seeds.
Authors F.Vallée, A.Kadziola, Y.Bourne, J.Abe, B.Svensson, R.Haser.
Ref. J Mol Biol, 1994, 236, 368-371.
PubMed id 8107117
Abstract
Secondary reference #2
Title 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.
Authors M.Søgaard, A.Kadziola, R.Haser, B.Svensson.
Ref. J Biol Chem, 1993, 268, 22480-22484.
PubMed id 7901200
Abstract
PROCHECK
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