Theoretical study on the chemical mechanism of enoyl-CoA hydratase and the form of inhibitor binding

Cui, Xiaobin; He, Rongxing; Yang, Qinlei; Shen, Wei; Li, Ming

doi:10.1007/s00894-014-2411-5

Cited by 2 publications

(2 citation statements)

References 45 publications

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“…理论上来说, 四元环过渡态的环张力较大, 使其在能量上很不稳定, 而且也不易被准确优化. 因此, DAC-CoA 水加成应该以分步机理而不是协同机理进行, 这与先前的理论计算结果保持一致 [18,19] . [13,16] [8,15] .…”

Section: 计算方法与模型unclassified

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Theoretical Insight into the Catalytic Mechanism of Enoyl-CoA Hydratase

Yu¹,

Xinya²,

Hui³

et al. 2017

Acta Chim. Sinica

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Enoyl-CoA hydratase (ECH), which is also known as crotonase, is the second requisite enzyme in the β-oxidation pathway of fatty acid that catalyzes the syn hydration of α,β-unsaturated thiolester substrates. In this work, ECH-catalyzed hydration mechanisms of DAC-CoA and Crotonyl-CoA were investigated using density functional theory (DFT) methods. Geometrical structures were optimized using Gaussian 03 program at the B3LYP/6-31G(d,p) level of theory. Frequency calculations were performed with the 6-31G(d,p) basis set to obtain zero-point vibrational energies (ZPEs) and to confirm the nature of all the stationary points that have no imaginary frequency for the local minima and have only one imaginary frequency for the saddle points. The single-point calculations on the optimized geometries were further performed with 6-311＋＋G(2d,2p) basis set to obtain more accurate energies. The polarizable-continuum model (PCM) with the dielectric constant of 4 was used to calculate the single point energies at 6-311＋＋G(2d, p) level on all the optimized geometries to consider the effects of enzymatic environment that was not included in the computational model. Given that B3LYP functional lacks the proper description of the long-range dispersion interactions, an empirical dispersion correction was further calculated using the DFT-D3 method to correct the B3LYP energies. The final energies reported in this work are the single-point energies corrected for ZPEs, solvation and dispersion effects. The calculated results suggested that hydration proceeds through a stepwise mechanism, involving an enolate intermediate. Glu164 functions as the sole base/acid for catalysis. Although Glu144 is not directly involved in hydration, it induces the catalytic water molecule to locate an ideal orientation to attack the double bond of substrate by the hydrogen-bonding interaction. Crotonyl-CoA shows higher hydration activity than DAC-CoA. The backbone NH groups of Ala98 and Gly141 form an oxyanion hole with substrate carbonyl oxygen, which play key roles in binding substrate and stabilizing the generated transition states and intermediates. In addition, the hydrogen-bonding networks surrounding Glu144 and Glu164 are of great importance for active site arrangement.

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Section: 计算方法与模型unclassified

“…Cui 等[19] 使用 DFT 方法考察了 Glu144 和 Glu164 不同质子化状态下的 DAC-CoA 水合活性, 研究发现 Glu144 和 Glu164 都应该以去质子化的状态存在. 不过, 严格来说由于共轭 π 键的存在, DAC-CoA 并不是 ECH 催化的理想底物, 不然实验上也很难得到 ECH-DAC-CoA 复合物的晶体结构.…”

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