Ordered Cleavage of Prothrombin by Prothrombinase Results from Constrained Binding and Preferential Active Site Engagement by One of the Two Cleavage Sites in Prothrombin.
Authors: Hacisalihoglu Ayse , Krishnaswamy Sriram 
Published: October 2019

Abstract
The conversion of prothrombin to thrombin is a paradigm for proteolytic activation reactions wherein product is produced following cleavage at more than one site in the substrate. Human prothrombinase catalyzes thrombin formation by sequential cleavage of prothrombin at Arg320 followed by cleavage at Arg271. The largely ordered activation arises because Arg320 in intact prothrombin is hydrolyzed by prothrombinase with a Vmax that is ~30-fold greater than that for cleavage at Arg271 while substrate affinity is unchanged. Paradoxically, this phenomenon has been proposed to arise from the constrained binding of prothrombin to prothrombinase. The alternate proposal is that two interconverting forms of the enzyme differentially recognize and cleave the two sites in prothrombin. We have investigated substrate binding using prothrombinase assembled with a catalytically inactive recombinant factor Xa (XaS195A) in which Ser195 was replaced with Ala and a series of recombinant variants of prothrombin. The prothrombin variants included wild type prothrombin (IIWT) containing both cleavage sites, IIQ271 with Arg271 replaced with Gln and a single cleavable site at Arg320, IIQ320 with Arg320 replaced with Gln and a single cleavable site at Arg271 and the uncleavable IIQQ containing both Gln substitutions. Titration of XaS195A assembled into prothrombinase with increasing concentrations of the fluorescent active site probe p-aminobenzamidine (PAB) produced a saturable increase in fluorescence confirming the expected ability of XaS195A to bind ligands, such as PAB, at the active site despite its lack of catalytic activity. The addition of a saturating concentration of IIWT to reaction mixtures containing PAB and prothrombinase assembled with XaS195A resulted in a decrease in PAB fluorescence arising from the engagement of the active site by the substrate and the associated displacement of PAB. Only a minor change in PAB fluorescence was observed with IIQQ even though this uncleavable derivative binds to prothrombinase with the same affinity as IIWT. Thus, features of the substrate-enzyme interaction that determine affinity are independent of active site engagement by the substrate. Saturating concentrations of IIQ271 displaced PAB from the active site of XaS195A within prothrombinase to the same extent observed with IIWT while essentially no fluorescence decrease was observed with IIQ320. It follows that although all prothrombin derivatives bind with similar affinity to prothrombinase, elements flanking Arg320 can readily engage the active site of XaS195A within the enzyme complex while those flanking the Arg271 site cannot. Our equilibrium binding measurements establish a primary role for active site binding in determining the perceived rate constant for catalysis without influencing substrate affinity. The differential action of prothrombinase on the two cleavage sites in prothrombin likely arises from constraints imposed by active site-independent interactions that drive substrate affinity and permit active site docking by the Arg320 site in the substrate but not the Arg271 site. These constraints in active site engagement explain asymmetry in the recognition of the two bonds in intact prothrombin and its ordered cleavage by prothrombinase.