Analysis of crystal structures of aspartic proteinases: On the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes

To elucidate the role of amino acid residues adjacent to the catalytic site of pepsin-like enzymes, we analyzed and compared the crystal structures of these enzymes, their complexes with inhibitors, and zymogens in the active site area (a total of 82 structures). In addition to the water molecule (W I) located between the active carboxyls and playing a role of the nucleophi le during catalytic reaction, another water molecule (W2) at the vicinity o f the active groups was found to be completely conserved. This water molecu le plays an essential role in formation of a chain of hydrogen-bonded resid ues between the active site flap and the active carboxyls on ligand binding . These data suggest a new approach to understanding the role of residues a round the catalytic site, which can assist the development of the catalytic reaction. The influence of groups adjacent to the active carboxyls is mani fested by pepsin activity at pH 1.0. Some features of pepsin-like enzymes a nd their mutants are discussed in the framework of the approach.