The structure of human pancreatic α‐amylase at 1.8 Å resolution and comparisons with related enzymes

The structure of human pancreatic α‐amylase has been determined to 1.8 Å resolution using X‐ray diffraction techniques. This enzyme is found to be composed of three structural domains. The largest is Domain A (residues 1–99, 169–404), which forms a central eight‐stranded parallel β‐barrel, to one end of which are located the active site residues Asp 197, Glu 233, and Asp 300. Also found in this vicinity is a bound chloride ion that forms ligand interactions to Arg 195, Asn 298, and Arg 337. Domain B is the smallest (residues 100–168) and serves to form a calcium binding site against the wall of the β‐barrel of Domain A. Protein groups making ligand interactions to this calcium include Asn 100, Arg 158, Asp 167, and His 201. Domain C (residues 405–496) is made up of anti‐parallel β‐structure and is only loosely associated with Domains A and B. It is notable that the N‐terminal glutamine residue of human pancreatic α‐amylase undergoes a posttranslational modification to form a stable pyrrolidone derivative that may provide protection against other digestive enzymes. Structure‐based comparisons of human pancreatic α‐amylase with functionally related enzymes serve to emphasize three points. Firstly, despite this approach facilitating primary sequence alignments with respect to the numerous insertions and deletions present, overall there is only ∼15% sequence homology between the mammalian and fungal α‐amylases. Secondly, in contrast, these same studies indicate that significant structural homology is present and of the order of ∼70%. Thirdly, the positioning of Domain C can vary considerably between α‐amylases. In terms of the more closely related porcine enzyme, there are four regions of polypeptide chain (residues 237–250, 304–310, 346–354, and 458–461) with significantly different conformations from those in human pancreatic α‐amylase. At least two of these could play a role in observed differential substrate and cleavage pattern specificities between these enzymes. Similarly, amino acid differences between human pancreatic and salivary α‐amylases have been localized and a number of these occur in the vicinity of the active site.