Proexosite I on prothrombin has been implicated in providing a recognition site for factor Va within prothrombinase. To examine whether hirudin-like sequences (659 -698) on the cofactor contribute to this interaction, we expressed and purified two-chain FVa derivatives that were intracellularly truncated at the C terminus of the heavy chain: Blood coagulation factor Va (FVa) 2 is a heterodimeric protein composed of a heavy chain (residues 1-709; 105 kDa) and a light chain (residues 1546 -2196; 74 kDa) which arises from limited proteolysis of the pro-cofactor factor V (FV) (1). Factor Va reversibly associates with the serine protease factor Xa (FXa) on an appropriate membrane surface in the presence of calcium ions to form prothrombinase. This enzyme complex cleaves two peptide bonds in prothrombin, resulting in the generation of ␣-thrombin (IIa) (2). This reaction is also catalyzed by membrane-bound FXa; however, incorporation of FVa within prothrombinase has a profound effect on the rate of IIa generation. Additionally, prothrombinase has remarkable specificity, as its only known biological substrate is prothrombin (2).Although the molecular basis underlying the rate-enhancing effect of FVa remains largely unknown, recent contributions have provided insight into how prothrombinase recognizes its protein substrate (3-5). These studies support a model in which binding specificity is determined by two resolvable steps involving an interaction at an exosite followed by active site docking. These exosites have yet to be fully defined, but there is some evidence that at least part of the enzyme exosite lies on the catalytic domain of FXa (6 -8). Because it is well established that prothrombin binds the cofactor (9 -16), this interaction may also play an important role in substrate recognition.There is increasing evidence that catalytic domain structures on prothrombin provide an exosite docking surface for prothrombinase (3,17,18). A series of observations suggest that the proexosite I region, the precursor site to IIa exosite I (19), contributes either directly or indirectly to this substrate binding site. For example, reagents that block proexosite I such as hirugen and bothrojaracin inhibit macromolecular substrate cleavage by prothrombinase or the FXa-FVa complex (3, 20, 21). Additionally, proexosite I prethrombin-1 mutants and a naturally occurring prothrombin variant (Arg 67 to His, chymotrypsin numbering system (22)) are poor substrates for prothrombinase and FXa-FVa (23, 24). Interestingly, these probes or mutations reduced the rate of IIa generation only in the presence of the cofactor, suggesting a link between FVa and proexosite I. Consistent with this, IIa exosite I mutants and exosite I probes inhibit FV activation (25-27). Additionally, detailed studies by Bock and co-workers have provided compelling evidence that the FVa heavy chain binds to exosite I of IIa (26,28). Taken together, these data are consistent with the idea that proexosite I plays an important role in macromolecular substrate recogniti...