Insights into the Reaction Mechanism of Aromatic Ring Cleavage by Homogentisate Dioxygenase: A Quantum Mechanical/Molecular Mechanical Study

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• 作者：Yue Qi ; Jiarui Lu ; Wenzhen Lai
• 刊名：Journal of Physical Chemistry B
• 出版年：2016
• 出版时间：May 26, 2016
• 年：2016
• 卷：120
• 期：20
• 页码：4579-4590
• 全文大小：920K
• 年卷期：0
• ISSN：1520-5207

文摘

To elucidate the reaction mechanism of the ring cleavage of homogentisate by homogentisate dioxygenase, quantum mechanical/molecular mechanical (QM/MM) calculations were carried out by using two systems in different protonation states of the substrate C₂ hydroxyl group. When the substrate C₂ hydroxyl group is ionized (the ionized pathway), the superoxo attack on the substrate is the rate-limiting step in the catalytic cycle, with a barrier of 15.9 kcal/mol. Glu396 was found to play an important role in stabilizing the bridge species and its O–O cleavage product by donating a proton via a hydrogen-bonded water molecule. When the substrate C₂ hydroxyl group is not ionized (the nonionized pathway), the O–O bond cleavage of the bridge species is the rate-limiting step, with a barrier of 15.3 kcal/mol. The QM/MM-optimized geometries for the dioxygen and alkylperoxo complexes using the nonionized model (for the C₂ hydroxyl group) are in agreement with the experimental crystal structures, suggesting that the C₂ hydroxyl group is more likely to be nonionized.