Model of a specific interaction: Salt-bridges form between prothrombin and its activating enzyme blood clotting factor Xa

In order for intricate biochemical pathways to function properly in the heterogeneous environment of a cell or organism, high specificity of enzymesubstrate reactions is essential. The molecular nature of this specificity is examined for the case of the specific activation of prothrombin by factor X_a of the blood coagulation system using model-building methods.The structure of blood clotting factor X_a was modeled by homology to the known structures of the mammalian serine proteases. The sequence about the cleaved peptide bond in prothrombin was placed into the active site of factor X_a in a conformation similar to that of bovine pancreatic trypsin inhibitor and soybean trypsin inhibitor, when bound to trypsin, and to that of the tripeptide chloromethyl ketones, when bound to γ-chymotrypsin and Streptomyces griseus protease B.The model of the complex between prothrombin and factor X_a shows the expected salt-bridge between the Arg preceding the cleaved peptide bond and the primary specificity residue Asp189 of factor X_a. Two other salt-bridges appear to be formed: between a Glu three residues before the cleaved bond in prothrombin and Arg143 of factor X_a, and between a second Glu three residues after the cleaved bond and Lys62 in factor X_a. Several hydrogen bonds and hydrophobic interactions also occur in the complex. A stereogeometric requirement for a Gly two residues before the cleaved bond is also imposed by the factor X_a structure.Examination of the known serine protease sequences and model building suggest that the two new salt-bridges are unique to the prothrombin-factor X_a complex. Therefore, these charge interactions, and the requirement for a Gly, are likely to be at least partially responsible for the high specificity of the activation of prothrombin by factor X_a.