Three dimensional structure of porcine pancreatic alpha‐amylase at 2.9 A resolution. Role of calcium in structure and activity

• Published in: The EMBO journal 1987-12, Vol.6 (13), p.3909-3916
• Main Authors: Buisson, G., Duée, E., Haser, R., Payan, F.
• Format: Article
• Language: English
• Subjects: alpha-Amylases - metabolism; Animals; Biochemistry, Molecular Biology; Biological and medical sciences; Calcium - metabolism; Crystalline structure; Fundamental and applied biological sciences. Psychology; Life Sciences; Models, Molecular; Molecular biophysics; Pancreas - enzymology; Protein Conformation; Structure in molecular biology; Swine; X-Ray Diffraction
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1002/j.1460-2075.1987.tb02731.x

The crystal structure of porcine pancreatic alpha‐amylase (PPA) has been solved at 2.9 A resolution by X‐ray crystallographic methods. The enzyme contains three domains. The larger, in the N‐terminal part, consists of 330 amino acid residues. This central domain has the typical parallel‐stranded alpha‐beta barrel structure (alpha beta)8, already found in a number of other enzymes like triose phosphate isomerase and pyruvate kinase. The C‐terminal domain forms a distinct globular unit where the chain folds into an eight‐stranded antiparallel beta‐barrel. The third domain lies between a beta‐strand and a alpha‐helix of the central domain, in a position similar to those found for domain B in triose phosphate isomerase and pyruvate kinase. It is essentially composed of antiparallel beta‐sheets. The active site is located in a cleft within the N‐terminal central domain, at the carboxy‐end of the beta‐strands of the (alpha beta)8 barrel. Binding of various substrate analogues to the enzyme suggests that the amino acid residues involved in the catalytic reaction are a pair of aspartic acids. A number of other residues surround the substrate and seem to participate in its binding via hydrogen bonds and hydrophobic interactions. The ‘essential’ calcium ion has been located near the active site region and between two domains, each of them providing two calcium ligands. On the basis of sequence comparisons this calcium binding site is suggested to be a common structural feature of all alpha‐amylases. It represents a new type of calcium‐protein interaction pattern.