Novel substrate specificity of designer 3-isopropylmalate dehydrogenase derived from Thermus thermophilus HB8

Redesigning of an enzyme for a new catalytic reaction and modified substrate specificity was exploited with 3-isopropylmalate dehydrogenase (IPMDH). Point-mutation on Gly-89, which is not in the catalytic site but near it, was done by changing it to Ala, Ser, Val, and Pro, and all the mutations changed the substrate specificity. The mutant enzymes showed higher catalytic efficiency (kcat/Km) than the native IPMDH when malate was used as a substrate instead of 3-isopropylmalate. More interestingly, an additional insertion of Gly between Gly-89 and Leu-90 significantly altered the substrate-specificity, although the overall catalytic activity was decreased. Particularly, this mutant turned out to efficiently accept D-lactic acid, which was not accepted as a substrate by wild-type IPMDH at all. These results demonstrate the opportunity for creating nove,enzymes by modification of amino acid residues that do not directly participate in catalysis, or by insertion of additional residues.

Tyr-139 in Thermus thermophilus 3-isopropylmalate dehydrogenase is involved in catalytic function

The role of Tyr-139, which is thought to be located at the active site of Thermus thermophilus HB8 3-isopropylmalate dehydrogenase, has been investigated by site-specific replacement with phenylalanine. The replacement scarcely affected the Michaelis constant (Km) for 3-isopropylmalate, but caused a 13-fold decrease of that for NAD. The catalytic constant (kcat) showed a 14-fold decrease. Accordingly, the catalytic efficiency (kcat/Km) decreased for 3-isopropylmalate but not for NAD. The results suggest that Tyr-139 is involved in the catalytic function through interaction with 3-isopropylmalate.

Kinetic analysis on the substrate specificity of 3-isopropylmalate dehydrogenase

Substrate specificity of 3-isopropylmalate dehydrogenase is analyzed using a series of synthetic (2R,3S)-3-alkylmalates. Each analog with hydrogen, methyl, ethyl, isopropyl, isobutyl, tert-butyl, and isoamyl group on C-3 functions as a substrate, implying a broad substrate specificity of the enzyme toward alkylmalates. The incremental binding energy of the isopropyl group of 3-isopropylmalate to the enzyme is estimated to be 3.55 kcal/mol, the rather small value supporting the broad specificity. Although the enzyme shows a broad specificity toward the alkylmalates, it does not show activity with isocitrate which has a negatively charged carboxymethyl group instead of the alkyl groups.