A stopped flow transient kinetic analysis of substrate binding and catalysis in Escherichia coli D-3-phosphoglycerate dehydrogenase

Pre-steady state, stopped flow analysis of Escherichia coli D-3-phosphoglycerate dehydrogenase was performed by following the fluorescence of protein tryptophan and the fluorescence resonance energy transfer from protein tryptophan to bound NADH. The results indicate that binding of substrates is ordered, with coenzyme, NADH, binding first. Furthermore, the analysis indicated that there are two sets of sites on the tetrameric enzyme that can be differentiated by their kinetic behavior. NADH binding was consistent with an initial binding event followed by a slow conformational change for each site. The slow conformational change is responsible for the apparent tight binding of NADH to the apoenzyme but is too slow to participate in the catalytic cycle when the enzyme is rapidly turning over. Subsequent binding of the substrate, α-ketoglutarate, was characterized by a rapid equilibrium binding event followed by a conformational change for each site. Catalysis in the direction of NAD⁺ reduction showed a distinct burst of activity followed by a slow rate of turnover, indicating that the rate-limiting step is after hydride transfer. Catalysis in the direction of NADH oxidation did not display burst kinetics, indicating that the rate-limiting step is at or before the hydride transfer step. The burst data indicated that the rate of NAD⁺ reduction (3.8 s^-1) is similar to the k_cat of the enzyme (2-3 s^-1) in that direction. However, analysis of the reaction with deuterated NADH failed to show an effect on the velocity of the reaction with a V_H/V_D = 1.07 ± 0.06. None of the other rates determined by stopped flow analysis could account for the k_cat of the enzyme in either direction (forward k _cat = 0.01 s^-1, reverse k_cat = 2-3 s ^-1), suggesting that the rate-limiting step in both directions is a conformational change in the enzyme that is not detected optically.