Global Kinetic Analysis of Mammalian E3 Reveals pH-dependent NAD+/NADH Regulation, Physiological Kinetic Reversibility, and Catalytic Optimum

• Published in: The Journal of biological chemistry Vol. 291; no. 6; pp. 2712 - 2730
• Main Authors: Moxley, Michael A., Beard, Daniel A., Bazil, Jason N.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 05-02-2016; American Society for Biochemistry and Molecular Biology
• Subjects: Animals; Dihydrolipoamide Dehydrogenase - chemistry; Dihydrolipoamide Dehydrogenase - metabolism; Enzyme Activation; enzyme kinetics; Enzymology; flavoprotein; global fitting; Hydrogen-Ion Concentration; kcat; Kinetics; mathematical modeling; mitochondrial metabolism; Mitochondrial Proteins - chemistry; Mitochondrial Proteins - metabolism; Muscle Proteins - chemistry; Muscle Proteins - metabolism; Myocardium - enzymology; NAD - chemistry; NAD - metabolism; pyruvate dehydrogenase complex (PDC); Swine; pyruvate dehydrogenase complex (PDC); flavoprotein; mathematical modeling; kcat; global fitting; enzyme kinetics; mitochondrial metabolism
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.M115.676619

Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD+/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD+ activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat.