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• W2394502486 endingPage "368" @default.
• W2394502486 startingPage "357" @default.
• W2394502486 abstract "We have determined the catalytic mechanism of the human cytosolic homodimeric isocitrate dehydrogenase (hICDH), an enzyme involved in the regulation of tumorogenesis. Our study constitutes the first theoretical attempt to describe the entire catalytic cycle of hICDH. In agreement with earlier experimental proposals, the catalysis was shown to proceed in three steps: (1) NADP+ reduction by the isocitrate substrate with the help of the Lys212B base, (2) β-decarboxylation of the resulting oxalosuccinate, generating an enolate, and (3) protonation of this intermediate by Tyr139A, giving rise to the α-ketoglutarate product. Our study supports that the β-decarboxylation of oxalosuccinate is the most likely rate-limiting step, with an activation Gibbs free energy of 16.5 kcal mol–1. The calculated values are in close agreement with the 16–17 kcal mol–1 range, derived by the application of transition state theory to the reaction rates determined experimentally (11 to 38 s–1). We emphasize the role of Mg2+ and Asp275A, whose acid/base properties throughout the catalytic cycle were found to lower the barrier to physiologically competent values. Aside from its chemical dual role (as a base, deprotonating Lys212B, and as an acid, protonating the basic Tyr139A deprotonated by the enolate intermediate), Asp275A also establishes hydrogen bonds with Arg132A and Tyr 139A that become shorter at critical transition states. These residues were shown to influence both the rate and the efficiency of hICDH. The knowledge drawn in this study provides new insights into future clinical and bioengineering applications of hICDH: namely, in the development of techniques to regulate the growth of glioblastomas and to capture and store carbon dioxide. Moreover, it further extends the comprehension of (1) the hydrogen/charge transfer mechanism that regulates the hydrogenation of NADP+ to NADPH, an ubiquitous biochemical reaction, and (2) the role of divalent metals as key structure elements in the family of NAD(P)+-dependent β-decarboxylases." @default.
• W2394502486 created "2016-06-24" @default.
• W2394502486 creator A5035051171 @default.
• W2394502486 creator A5048088473 @default.
• W2394502486 creator A5072586254 @default.
• W2394502486 date "2015-12-15" @default.
• W2394502486 modified "2023-10-15" @default.
• W2394502486 title "Unveiling the Catalytic Mechanism of NADP⁺-Dependent Isocitrate Dehydrogenase with QM/MM Calculations" @default.
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• W2394502486 doi "https://doi.org/10.1021/acscatal.5b01928" @default.
• W2394502486 hasPublicationYear "2015" @default.
• W2394502486 type Work @default.
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