Factor VIIa: Difference between revisions

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===Catalytic domain===

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 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(195) then attacks the scissile bond of the substrate. The general base His193(57) transfers the abstracted 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(57) abstracts a proton from water as it attacks the acylenzyme to again form a tetrahedral intermediate. His193(57) then acts as an acid and protonates Ser344(195) releasing the product acid and regenerates the enzyme. This reaction is largely possible by having a His193(57) with a pKa ~7 necessary for deprotonation, a hydrogen bonding network or “the charge relay system” activating Ser344(195) for nucleophilic attack, stabilization of the negatively charged oxyanion of the tetrahedral intermediate by the main chain NHs of Ser344(195) and Gly342(193). [[Image:mechanism ser-protease.jpg|left]] [[Image:catalytic triad.jpg|~~right~~]]

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(195) then attacks the scissile bond of the substrate. The general base His193(57) transfers the abstracted 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(57) abstracts a proton from water as it attacks the acylenzyme to again form a tetrahedral intermediate. His193(57) then acts as an acid and protonates Ser344(195) releasing the product acid and regenerates the enzyme. This reaction is largely possible by having a His193(57) with a pKa ~7 necessary for deprotonation, a hydrogen bonding network or “the charge relay system” activating Ser344(195) for nucleophilic attack, stabilization of the negatively charged oxyanion of the tetrahedral intermediate by the main chain NHs of Ser344(195) and Gly342(193). [[Image:mechanism ser-protease.jpg|left]]

[[Image:catalytic triad.jpg|left]]

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

The charge relay system explains the action of Ser344 as part of resonance forms Asp-CO2-/H-His/Ser-OH and Asp-CO2H/His-H/Ser-O which involve proton transfers between Ser344 to His193 and His193 to Asp242. However this two-proton transfer mechanim requires that the pKa of His344 is lower than pKa of Asp242. The argument for one-proton transfer mechanism, supported by 1H NMR experiments, observed the pKa of free enzyme and acylenzyme His193 to be ~7 whereas that of tetrahedral intermediate to be more than 10. This argues for electrostatic stabilization of protonated His193 by the negatively charged Asp242 or a one-proton transfer mechanims<ref>PMID:12475199</ref>.

Factor VIIa: Difference between revisions

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 ===Catalytic domain===
 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 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(195) then attacks the scissile bond of the substrate. The general base His193(57) transfers the abstracted 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(57) abstracts a proton from water as it attacks the acylenzyme to again form a tetrahedral intermediate. His193(57) then acts as an acid and protonates Ser344(195) releasing the product acid and regenerates the enzyme. This reaction is largely possible by having a His193(57) with a pKa ~7 necessary for deprotonation, a hydrogen bonding network or “the charge relay system” activating Ser344(195) for nucleophilic attack, stabilization of the negatively charged oxyanion of the tetrahedral intermediate by the main chain NHs of Ser344(195) and Gly342(193).    [[Image:mechanism ser-protease.jpg|left]] [[Image:catalytic triad.jpg|right]]
+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(195) then attacks the scissile bond of the substrate. The general base His193(57) transfers the abstracted 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(57) abstracts a proton from water as it attacks the acylenzyme to again form a tetrahedral intermediate. His193(57) then acts as an acid and protonates Ser344(195) releasing the product acid and regenerates the enzyme. This reaction is largely possible by having a His193(57) with a pKa ~7 necessary for deprotonation, a hydrogen bonding network or “the charge relay system” activating Ser344(195) for nucleophilic attack, stabilization of the negatively charged oxyanion of the tetrahedral intermediate by the main chain NHs of Ser344(195) and Gly342(193).    [[Image:mechanism ser-protease.jpg|left]]
+[[Image:catalytic triad.jpg|left]]
 ====One-proton versus Two-proton transfer====
 The charge relay system explains the action of Ser344 as part of resonance forms Asp-CO2-/H-His/Ser-OH and Asp-CO2H/His-H/Ser-O which involve proton transfers between Ser344 to His193 and His193 to Asp242. However this two-proton transfer mechanim requires that the pKa of His344 is lower than pKa of Asp242. The argument for one-proton transfer mechanism, supported by 1H NMR experiments, observed the pKa of free enzyme and acylenzyme His193 to be ~7 whereas that of tetrahedral intermediate to be more than 10. This argues for electrostatic stabilization of protonated His193 by the negatively charged Asp242 or a one-proton transfer mechanims<ref>PMID:12475199</ref>.