Role of Leu99 of thrombin in determining the P2 specificity of serpins

A recent study indicated that Tyr99 (chymotrypsin numbering) of factor Xa and Thr99 of activated protein C are S2 subsite residues that determine the P2 specificity of their substrates and inhibitors. To investigate the contribution of Leu99 to the P2 binding specificity of thrombin, three mutants of thrombin were prepared in which Leu99 was substituted with Tyr (L99Y), Thr (L99T), or Gly (L99G). Kinetic analysis indicated that antithrombin (AT with P2 Gly) inhibited thrombin L99Y, 14.1- and 5.5-fold slower than thrombin in the absence and presence of heparin, respectively. The L99Y mutation increased the stoichiometry of AT inhibition in the presence of heparin from similar to 1.6 to similar to 4.6, indicating that L99Y recognized AT as a substrate. The inhibition rates of L99T and L99G by AT, respectively, were 500.0-and 916.7-fold slower than thrombin in the absence of heparin but only 41.8- and 64.5-fold slower than thrombin in the presence of heparin. Resolution of the two-step reactions of AT with the mutant thrombins revealed that the impaired reactivities occurred in the second reaction step in which a non-covalent AT-thrombin encounter complex is converted to a stable, covalent complex. In reactions with protein C inhibitor (PCI with P2 Phe), L99Y was inhibited 3.5-fold slower than thrombin, L99T was inhibited at a similar or faster rate, and L99G was inhibited 23.9-fold faster than thrombin. The epidermal growth factor-like domains 4-6 of thrombomodulin (TM4-6) accelerated the PCI inhibition of wild-type and L99G thrombins 73.9- and 5.3-fold, respectively. Further studies indicated that the fibrinogen clotting and protein C activation rates by the mutants were impaired, but the cofactor function of TM was not affected as TM4-6 bound to wild-type [K-d(app) = 5.9 nM] and mutant thrombins with similar affinities [K-d(app) = 4.4-6.9 nM] and enhanced protein C activation rates by all mutants effectively. These results indicate that (1) Leu99 of thrombin is critical for determination of the P2 specificity of serpins, AT and PCI, (2) increasing the polarity of the S2 pocket of thrombin by introduction of a hydrophilic residue into this pocket is detrimental for reaction with AT, but it is tolerated in reaction with PCI, so that only the size of the S2 pocket of thrombin determines the P2 specificity of PCI, and (3) the thrombomodulin-induced conformational change that results in acceleration of thrombin inhibition by PCI involves Leu99.