Factor VIIa: Difference between revisions

There are three steps serine proteases take to hydrolyze an amide bond: 1)activation of amide bonds by the interaction of the general acid with the carbonyl oxygen of the substrtate amide bond which disrupts resonance stabilization 2) activation of water by general base 3)activation of amines by protonation before expulsion. Serine proteases hydrolyze amide bonds with rates of 10^10–fold higher than the uncatalyzed reactions.   

In FVIIa Ser344(195) of the catalytic triad is activated by a His193(57), or the general base, which itself is stabilized by a hydrogen bond to Asp242(102). These reactions result in a formation of a tetrahedral intermediate and the oxyanion hole. The oxyanion hole is stabilized by interactions with main chain NHs. The activated Ser344 then attacks the scissile bond of the substrate. The general base His193 transfers the abstracterd proton from Ser to the amine leaving group, the tetrahedral intermediate (transition state) collapses and an acylenzyme intermediate is formed releasing the product. The general base His193 abstracts a proton from water as it attacks the acylenzyme to again form a tetrahedral intermediate. His193 then acts as an acid and protonates Ser344 releasing the product acid and regenerates the enzyme. This reaction is largely possible by having a His193 with a pKa ~7 necessary for deprotonation15, a hydrogen bonding network or “the charge relay system” activating Ser344 for nucleophilic attack, stabilization of the negatively charged oxyanion of the tetrahedral intermediate by the main chain NHs of Ser344 and Gly342(193). The kinetics are described in three steps: 1) binding of enzyme to substrate (k+1, k-1), 2) acylation of enzyme (k2), and 3) deacylation (k3)  

====One-proton versus Two-proton transfer====

All of the serine proteases have a catalytic domain consisting of two β-barrels with the catalytic triad, Ser-His-Asp located at the interface<ref>PMID:9374470</ref>. Five enzyme-substrate hydrogen bonds at positions P1 and P3 are well conserved and serve to position the scissile peptide bond in the correct orientation for an attack by the γ-oxygen of Ser. More distal contacts diverge. Mutational experiments have shown that the S1 pocket is important in organization of the substrate for catalysis. Divergent evolution[http://en.wikipedia.org/wiki/Divergent_evolution]enabled mammals to possess multiple enzymes with specific roles. Earlier organisms, bacteria and prokaryotes, possess broad specificities of the active site where more distant residues play a bigger role in substrtate recognition<ref>PMID:2716847</ref>. The most divergent are the surface loops which control specificity. Serine proteases not only show the divergence of substrate specificity but also examples of convergent evolution[http://en.wikipedia.org/wiki/Convergent_evolution].  A demonstration of convergent evolution in serine proteases is found in four other folds, besides the chynotrypsin-like fold, with the catalytic triad in similar positions<ref>PMID:879782</ref>.