Structural basis for the inhibition of porcine pepsin by Ascaris pepsin inhibitor-3

The three-dimensional structures of pepsin inhibitor-3 (PI-3) from Ascaris suum and of the complex between PI-3 and porcine pepsin at 1.75 Angstrom an d 2.45 Angstrom resolution, respectively, have revealed the mechanism of as partic protease inhibition by this unique inhibitor. PI-3 has a new fold co nsisting of two domains, each comprising an antiparallel beta-sheet flanked by an alpha-helix. In the enzyme-inhibitor complex, the N-terminal beta-st rand of PI-3 pairs with one strand of the 'active site flap' (residues 70-8 2) of pepsin, thus forming an eight-stranded beta-sheet that spans the two proteins. PI-3 has a novel mode of inhibition, using its N-terminal residue s to occupy and therefore block the first three binding pockets in pepsin f or substrate residues C-terminal to the scissile bond (S1'-S3'). The molecu lar structure of the pepsin-PI-3 complex suggests new avenues for the ratio nal design of proteinaceous aspartic proteinase inhibitors.