Inhibition and alternate-substrate studies on the mechanism of malic enzyme

A number of dead-end inhibitors and alternate substrates were examined to gain an understanding of the substrate specificity and mechanism of malic enzyme. Comparison of Ki values for competitive inhibitors suggested that binding of the l-carboxyl of L-malate is by ion pairing with lysine or arginine, while binding of the 4-carboxyl is weaker, and probably of the induced-dipolar type. The 2-hydroxyl hydrogen bonds to a catalytic group, which, when it is protonated, adsorbs the keto form of oxalacetate. Since the only molecule other than L-malate that is oxidized is L-malate-beta-amide, carbon 4 must be trigonal for substrate activity, although a tetrahedral carbon bearing one or two hydroxyl groups gives good binding. Hydroxy groups at carbon 3 contribute to binding, but prevent substrate activity. Hydroxy and ketomalonates are bound more strongly than any of the four carbon acids, suggesting that the latter are bound with some strain. In inhibition studies, pyruvate analogues were competitive vs. pyruvate but noncompetitive vs. malate, while malate analogues were competitive vs. malate and noncompetitive vs. pyruvate. These compounds thus bind to both enzyme-triphosphopyridine nucleotide (E-TPN) and enzyme-reduced triphosphopyridine nucleotide (E-TPNH), but only malate analogues prevent release of TPN, while pyruvate analogues prevent release of TPNH. Ketomalonate and oxalacetate, both of which are slowly reduced by the enzyme in the presence of TPNH and thus must combine in the keto form with E-TPNH,, appear to combine with E-TPN mainly in the gem-diol (or for oxalacetate, also the enol) form. The substrate for the decarboxylation of oxalacetate at pH 4.5 is the keto form.