Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis

Palló, A; Oláh, J [Oláh, Julianna (Bioszervetlen kém...), szerző] Szervetlen és Analitikai Kémia Tanszék (BME / VBK); Gráczer, E [Gráczer, Éva Laura (Enzimológia), szerző] Enzimológiai Intézet (TTK); Merli, A; Závodszky, P [Závodszky, Péter (Molekuláris immun...), szerző] Enzimológiai Intézet (TTK); Weiss, MS ✉; Vas, M ✉ [Kazinczyné Vas, Mária (Enzimológia), szerző] Enzimológiai Intézet (TTK)

Angol nyelvű Tudományos Szakcikk (Folyóiratcikk)
Megjelent: FEBS JOURNAL 1742-464X 1742-4658 281 (22) pp. 5063-5076 2014
  • SJR Scopus - Biochemistry: Q1
    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.
    Hivatkozás stílusok: IEEEACMAPAChicagoHarvardCSLMásolásNyomtatás
    2022-01-23 01:09