Pyridoxal phosphate (PLP) dependent enzymes are ubiquitous in nitrogen metabolism and catalyze many medically important transformations. As a group, they catalyze an extraordinarily wide variety of reactions. A fundamental question bearing on inhibitor design is how a given apoenzyme determines a unique reaction specificity. Dialkylglycine decarboxylase (DGD) is an unusual PLP dependent enzyme that rapidly catalyzes both decarboxylation and transamination in its normal catalytic cycle. This allows the quantitation of stereoelectronic effects, which are a primary mechanism for determining PLP reaction specificity. Oxidative decarboxylation specificity is achieved in DGD via a concerted decarboxylation/proton transfer transition state. The energetic requirements of this concerted transition state will be determined. Additionally, DGD has two alkali metal ion binding sites, one of which binds a variety of ions and controls activity. Understanding the mechanism by which specificity for alkali metal ions is achieved has broad physiological significance. Alanine racemase is the prototypical PLP dependent racemase, which provides D-alanine for bacterial cell wall biosynthesis. This enzyme is extremely fast (about 20,000 s[-1]) at deprotonating carbon and shows extraordinarily fidelity. It is hypothesized that these are a result of a concerted double proton transfer transition state. This hypothesis will be tested. Additionally, the free energy profile for alanine racemase will be determined by straightforward kinetic analyses as a function of the fundamental extrinsic variables (e.g. pH, salt, temperature) controlling enzyme activity, providing insight into the origins of energy barriers in enzymatic reactions. Human serine racemase provides D-serine in the brain, which is a coactivator of the NMDA receptor. This enzyme will be compared mechanistically with alanine racemase and examined as a target for drugs to prevent stroke damage. Lastly, the electrophilic requirements of PLP enzymes will be determined through a collaborative 15N NMR study in which the protonation state of active site nitzogens of PLP enzymes is determined, and additionally by using isosteric coenzyme analogs.
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