THE ACTIVE-CENTER OF A MAMMALIAN ALPHA-AMYLASE - STRUCTURE OF THE COMPLEX OF A PANCREATIC ALPHA-AMYLASE WITH A CARBOHYDRATE INHIBITOR REFINED TO 2.2-ANGSTROM RESOLUTION

An X-ray structure analysis of a crystal of pig pancreatic alpha-amyla se (EC 3.2.1.1) that was soaked with acarbose (a pseudotetrasaccharide alpha-amylase inhibitor) showed electron density corresponding to fiv e fully occupied subsites in the active site. The crystal structure wa s refined to an R-factor of 15.3%, with a root mean square deviation i n bond distances of 0.015 Angstrom, The model includes all 496 residue s of the enzyme, one calcium ion, one chloride ion, 393 water molecule s, and five bound sugar rings. The pseudodisaccharide acarviosine that is the essential structural unit responsible for the activity of all inhibitors of the acarbose type was located at the catalytic center. T he carboxylic oxygens of the catalytically competent residues Glu233 a nd Asp300 form hydrogen bonds with the ''glycosidic'' NH group of the acarviosine group. The third residue of the catalytic triad Asp197 is located on the opposite side of the inhibitor binding cleft with one o f its carbonyl oxygens at a 3.3-Angstrom distance from the anomeric ca rbon C-1 of the inhibitor center. Binding of inhibitor induces structu ral changes at the active site of the enzyme. A loop region between re sidues 304 and 309 moves in toward the bound saccharide, the resulting maximal mainchain movement being 5 Angstrom for His305. The side chai n of residue Asp300 rotates upon inhibitor binding and makes strong va n der Waals contacts with the imidazole ring of His299. Four histidine residues (His101, His201, His299, and His305) are found to be hydroge n-bonded with the inhibitor. Many protein-inhibitor hydrogen bond inte ractions are observed in the complex structure, as is clear hydrophobi c stacking of aromatic residues with the inhibitor surface. The chlori de activator ion and structural calcium ion are hydrogen-bonded via th eir ligands and water molecules to the catalytic residues.