NEW INSIGHTS INTO THE REGULATION OF THE BLOOD-CLOTTING CASCADE DERIVED FROM THE X-RAY CRYSTAL-STRUCTURE OF BOVINE MEIZOTHROMBIN DES F1 IN COMPLEX WITH PPACK

Background: The conversion of prothrombin to thrombin by factor Xa is the penultimate step in the blood clotting cascade. In vivo, where the conversion occurs primarily on activated platelets in association wit h factor Va and Ca2+ ions, meizothrombin is the major intermediate of the two step reaction, Meizothrombin rapidly loses the fragment 1 doma in (F1) by autolysis to become meizothrombin des F1 (mzTBN-F1). The ph ysiological properties of mzTBN-F1 differ dramatically from those of t hrombin due to the presence of prothrombin fragment 2 (F2), which rema ins covalently attached to the activated thrombin domain in mzTBN-F1. Results: The crystal structure of mzTBN-F1 has been determined al 3.1 Angstrom resolution by molecular replacement, using only the thrombin domain, and refined to R and R-free values of 0.205 and 0.242, respect ively. The protease active site was inhibited with o-Phe-Pro-Arg-chlor omethylketone (PPACK) to reduce autolysis. The mobile linker chain con necting the so-called kringle and thrombin domains and the first two N -acetylglucosamine residues attached to the latter were seen in electr on-density maps improved with the program SQUASH. Previously these reg ions had only been modeled. Conclusions: The F2 kringle domain in mzTB N-F1 is bound to the electropositive heparin-binding site on thrombin in an orientation that is systematically shifted and has significantly more interdomain contacts compared to a noncovalent complex of free F 2 and free thrombin. F2 in mzTBN-F1 forms novel hydrogen bonds to the carbohydrate chain of thrombin and perhaps stabilizes a unique, rigid conformation of the gamma-autolysis loop through non-local effects. Th e F2 linker chain, which does not interfere with the active site or fi brinogen-recognition site, is arranged so that the two sites cleaved b y factor Xa are separated by 36 Angstrom. The two mzTBN-F1 molecules i n the asymmetric unit share a tight 'dimer' contact in which the activ e site of one molecule is partially blocked by the F2 kringle domain o f its partner. This interaction suggests a new model for prothrombin o rganization.