Human alpha-thrombin inhibition by the active site titrant Nalpha-(N,N-dimethylcarbamoyl)-alpha-azalysine-p-nitrophenyl-ester: a comparative kinetic and x-ray crystallographic study

Kinetics for the hydrolysis of the chromogenic active site titrant Nα-(N,N-dimethylcarbamoyl)-α-azalysine p-nitrophenyl ester (Dmc-azaLys-ONp) catalyzed by bovine β-trypsin, bovine α-thrombin, human α-thrombin, human Lys77-plasmin, human urinary kallikrein, the M_r 33,000 and M_r 54,000 species of human urokinase, as well as by porcine pancreatic β-kallikrein-A and B have been obtained between pH 6.0 and 8.0, at 21.0 °C. Moreover, the three dimensional structure of the human α-thrombin-(hirugen)·Dmc-azaLys acyl·enzyme complex has been analyzed and refined by X-ray crystallography at 2.0 Å resolution (R-factor = 0.168). As observed for bovine β-trypsin, the acylating inhibitor molecule is covalently bound to the Ser195 catalytic residue, filling the human α-thrombin S₁ primary specificity subsite with its lysyl side-group. However, the carbonyl group of the scissile human α-thrombin·Dmc-azaLys acyl bond does not occupy properly the oxyanion binding hole. At variance from the bovine β-trypsin·Dmc-azaLys acyl·enzyme structure, a second, not covalently bound, inhibitor molecule, partly shielded by the 60-insertion loop of human α-thrombin, is contacting the enzyme "aryl-binding site".