Abstract
Factor Xa (FXa) hydrolyzes two peptide bonds in prothrombin having (Glu/Asp)-Gly-Arg-(Thr/Ile) for P(3)-P(2)-P(1)-P(1)' residues, but the exact preferences of its catalytic groove remain largely unknown. To investigate the specificity of FXa, we synthesized full sets of fluorescence-quenched substrates carrying all natural amino acids (except Cys) in P(3), P(2), P(1)', P(2)', and P(3)' and determined the k(cat)/K(m) values of cleavage. Contrary to expectation, glycine was not the "best" P(2) residue; peptide with phenylalanine was cleaved slightly faster. In fact, FXa had surprisingly limited preferences, barely more pronounced than trypsin; in P(2), the ratio of the k(cat)/K(m) values for the most favorable side chain over the least was 289 (12 with trypsin), but in P(1)', this ratio was only 30 (versus 80 with trypsin). This unexpected selectivity undoubtedly distinguished FXa from thrombin, which exhibited ratios higher than 19,000 in P(2) and P(1)'. Thus, with respect to the catalytic groove, FXa resembles a low efficiency trypsin rather than the highly selective thrombin. The rates of cleavage of the peptidyl substrates were virtually identical whether or not FXa was in complex with factor Va, suggesting that the cofactor did not exert a direct allosteric control on the catalytic groove. We conclude that the remarkable efficacy of FXa within prothrombinase originates from exosite interaction(s) with factor Va and/or prothrombin rather than from the selectivity of its catalytic groove.
Highlights
At the confluence of the formerly named intrinsic and extrinsic pathways, factor Xa (FXa)1 is the midway protease of the blood clotting waterfall [1]
We conclude that the remarkable efficacy of Factor Xa (FXa) within prothrombinase must rely on exosite(s) interaction(s) rather than on a purely allosteric mechanism involving its catalytic groove
By using a collection of fluorescence-quenched substrates, our study provides a precise and complete mapping of FXa subsites
Summary
At the confluence of the formerly named intrinsic and extrinsic pathways, factor Xa (FXa) is the midway protease of the blood clotting waterfall [1]. Tissue factor pathway inhibitor (TFPI) does not require any cofactor to rapidly neutralize FXa [8]. FXa catalyzes a number of other reactions: activation of factor VII in a positive feedback within the tissue factor pathway [9], activation of factors V [10] and VIII [11], cleavage of protease-activated receptor 2 [12], and neutralization of protein S, albeit only in the presence of phospholipid and calcium [13]. In contrast to FXa, thrombin alone rapidly catalyzes a number of critical reactions in the cascade: cleavage of fibrinogen, activation of factors V and VIII, and activation of protease-activated receptor 1 [6, 10, 15]. We conclude that the remarkable efficacy of FXa within prothrombinase must rely on exosite(s) interaction(s) rather than on a purely allosteric mechanism involving its catalytic groove
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