X-ray crystallographic determination of the structure of bovine lens leucine aminopeptidase complexed with amastatin: formulation of a catalytic mechanism featuring a gem-diolate transition state.

The structure of the complex of bovine lens leucine aminopeptidase (blLAP) with the slow-, tight-binding inhibitor amastatin has been determined by X-ray crystallography. X-ray diffraction data were collected at -150 degrees C from a single blLAP-amastatin crystal which under the data collection conditions was of the space group P6(3)22 with unit cell parameters a = 130.3 A and c = 121.9 A. The structure of the blLAP-amastatin complex was determined by molecular replacement, using the structure of native blLAP as the starting model. Refinement of the blLAP-amastatin model plus 132 water molecules against data from 10.0- to 2.4-A resolution resulted in a final structure with a crystallographic residual of 0.198. The binding mode of amastatin is similar to that of bestatin, the structure of whose complex with blLAP has previously been determined. Of particular note, the N-terminus-to-C-terminus orientation of the two bound inhibitors is the same. The two N-terminal residues of amastatin and bestatin occupy the same binding sites, which are most likely S1 and S'1. The slow binding of amastatin and bestatin may be partially attributable to a binding mechanism in which the two active site metals are sequentially coordinated by the P1 amino and hydroxyl groups of these inhibitors. A catalytic mechanism for blLAP is proposed based on the binding modes of amastatin and bestatin and plausible binding modes of a dipeptide substrate and its putative gem-diolate transition state which were modeled into the active site of blLAP after the binding mode of amastatin. The proposed catalytic mechanism invokes roles for the catalytic metals in binding and activating the substrate and in stabilizing the transition state. The mechanism also includes roles for Asp-255 as a general base, Arg-336 as an additional electrophilic substrate activator and transition state stabilizer, and Lys-262 as a proton shuttle.