Structure of the Rhizomucor miehei aspartic proteinase complexed with the inhibitor pepstatin A at 2.7 Å resolution

Crystals of Rhizomucor miehei aspartic proteinase (RMP) complexed with pepstatin A grew in the orthorhombic space group P2₁2₁2₁ and were isomorphous to native RMP crystals. The unit-cell dimensions are a = 41.52, b = 50.82, c = 172.71 Å. There is one RMP-pepstatin A complex per asymmetric unit. The structure of the RMP-pepstatin A complex has been refined to a crystallographic R value of 19.3% and an R_free value of 28.0% at 2.7 Å resolution. A pepstatin A molecule fits into the large substrate-binding cleft between the two domains of RMP in an extended conformation up to the alanine residue at the P2' position. The dipeptide analogue statine residue at the P3'-P4' position forms an inverse [gamma]-turn (P3'-P1') with the statine residue at the P1-P1' position and its leucyl side chain binds back into the S1' subsite. The inhibitor interacts with the residues of the substrate-binding pocket by both hydrogen bonds and hydrophobic interactions. The hydroxyl group of the statine residue at the P1-P1' position forms hydrogen bonds with both catalytic aspartate residues (Asp38 and Asp237). This conformation mimics the expected transition state of the enzyme-substrate interaction. The binding of the inhibitor to the enzyme does not produce large distortions of the active site. No domain movement was observed compared with the native enzyme structure. However, the surface-flap region (residues 82-88) undergoes a conformational change, moving toward the inhibitor and becoming rigid owing to the formation of hydrogen bonds with the inhibitor. B-factor calculations of the two domains suggest that the C-terminal domain becomes more rigid in the complex than in the native structure.