Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis

Palló, Anna and Oláh, Julianna and Gráczer, Éva Laura and Merli, Angelo and Závodszky, Péter and Kazinczyné Vas, Mária (2014) Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. FEBS JOURNAL, 281 (22). pp. 5063-5076. ISSN 1742-464X


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The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn2+, its substrate isopropylmalate and its co-factor product NADH at 2.0 Å resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 Å. The structure further shows binding of a K+ ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD+ is easily possible, with an activation energy of approximately 15 kcal·mol-1. The activation energy increases by approximately 4-6 kcal·mol-1 when the K+ ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the ε-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule.

Item Type: Article
Uncontrolled Keywords: Thermus thermophilus; nonhuman; enzyme structure; enzyme conformation; enzyme binding; enzyme active site; CATALYSIS; carboxy terminal sequence; calculation; ARTICLE; reduced nicotinamide adenine dinucleotide; PYRIDINE; potassium ion; Manganese; 3 isopropylmalate dehydrogenase; X-RAY CRYSTALLOGRAPHY; QM/MM calculations; Oxidative decarboxylation; ISOPROPYLMALATE DEHYDROGENASE; general base catalysis
Subjects: Q Science / természettudomány > QH Natural history / természetrajz > QH301 Biology / biológia > QH3011 Biochemistry / biokémia
Depositing User: MTMT SWORD
Date Deposited: 03 Dec 2014 09:24
Last Modified: 01 Nov 2015 00:15

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