Exosite 1 of thrombin consists of a cluster of basic residues (Arg-35, Lys-36, Arg-67, Lys-70, Arg-73, Arg-75, and Arg-77 in chymotrypsinogen numbering) that play key roles in the function of thrombin. Structural data suggest that the side chain of Arg-35 projects toward the active site pocket of thrombin, but all other residues are poised to interact with thrombomodulin (TM). To study the role of these residues in TM-mediated protein C (PC) activation by thrombin, a charge reversal mutagenesis approach was used to replace these residues with a Glu in separate constructs. The catalytic properties of the mutants toward PC were analyzed in both the absence and presence of TM and Ca 2؉ . It was discovered that, with the exception of the Arg-67 and Lys-70 mutants, all other mutants activated PC with similar maximum rate constants in the presence of a saturating concentration of TM and Ca 2؉ , although their affinity for interaction with TM was markedly impaired. The catalytic properties of the Arg-35 mutant were changed so that PC activation by the mutant no longer required Ca 2؉ in the presence of TM, but, instead, it was accelerated by EDTA. Moreover, the activity of this mutant toward PC was improved Ϸ25-fold independent of TM. These results suggest that Arg-35 is responsible for the Ca 2؉ dependence of PC activation by the thrombin-TM complex and that a function for TM in the activation complex is the allosteric alleviation of the inhibitory interaction of Arg-35 with the substrate. P rotein C (PC) is a multidomain vitamin K-dependent plasma serine protease zymogen that, on activation by thrombin in complex with thrombomodulin (TM), down-regulates the coagulation cascade by inactivating factors Va and VIIIa by limited proteolysis (1-3). Similar to the structures of other vitamin K-dependent coagulation proteases, the structure of PC consists of an amino-terminal ␥-carboxyglutamic residue (Gla) domain followed by two epidermal growth factor (EGF)-like domains, and a C-terminal catalytic domain with a trypsin-like primary specificity pocket (4, 5). The Gla domain contains several cooperative low-affinity Ca 2ϩ -binding sites, which mediate the metal ion-dependent interaction of PC with endothelial protein C receptor and the thrombin-TM complex on membrane surfaces (1, 6). In addition to the Gla domain, the amino-terminal EGF domain and the catalytic domain of PC each have a high-affinity Ca 2ϩ -binding site with important roles for the structure and function of the protein (4, 7). The Ca 2ϩ -binding site on the protease domain of PC is located on the 70-80 loop (7). With the exception of prothrombin, the same loop is also known to bind Ca 2ϩ in other vitamin K-dependent coagulation proteases (8, 9) and in trypsin (10). The binding of Ca 2ϩ to this loop plays a complex role in PC activation by thrombin: it is inhibitory for activation by thrombin alone but stimulatory for activation by the thrombin-TM complex (11). The Ca 2ϩ -binding site in the amino-terminal domain does not appear to play a role in PC activation ...