A DFT Study of Nucleobase Dealkylation by the DNA Repair Enzyme AlkB
A DFT Study of Nucleobase Dealkylation by the DNA Repair Enzyme AlkB
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DOI：
10.1021/jp810715t
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发表时间：
2009-04-09
影响因子：
3.3
通讯作者：
Gauld, James W.
中科院分区：
文献类型：
--
作者：
Liu, Haining;Llano, Jorge;Gauld, James W.
氧化脱烷基化是在α-酮戊二酸-Fe（II）-依赖性AlkB酶家族中发现的一种独特的机制途径，以去除对DNA碱基的烷基化损伤并使核碱基再生至其天然状态。采用密度泛函B3 LYP方法结合自洽反应场，研究了AlkB多步催化机理的三重态、五重态和七重态自旋势能面.该机制被认为是由四个阶段。首先，在活性位点复合物中，分子氧与铁的结合与电子转移协同发生，从而产生铁-超氧化物物种。第二，竞争引发的氧的活化，以产生高价的铁-氧中间体（ferryloxo Fe-IV=O和ferric-oxyl Fe-III-O-中心点物种）被发现发生在五重态和七重态表面。然后，发现活化的铁氧配体的构象重新取向是近热中性的，势垒约为。50 W mol（-1）。最后阶段是受损核碱基的氧化脱烷基化，其中速率控制步骤是通过ferryloxo配体从破坏性甲基中提取氢原子。计算的势垒为87.4 kJ mol（-1），与实验的活化能约为1.4kJ mol（-1）符合得很好。83 kJ mol（-1）。
Oxidative dealkylation is a unique mechanistic pathway found in the alpha-ketoglutarate-Fe(II)-dependent AlkB family of enzymes to remove the alkylation damage to DNA bases and regenerate nucleobases to their native state. The B3LYP density functional combined with a self-consistent reaction field was used to explore the triplet, quintet, and septet spin-state potential energy surfaces of the multistep catalytic mechanism of AlkB. The mechanism was found to consist of four stages. First, binding of dioxygen to iron in the active-site complex occurs concerted with electron transfer, thereby yielding a ferric-superoxido species. Second, competing initiation for the activation of oxygen to generate the high-valent iron-oxygen intermediates (ferryloxo Fe-IV=O and ferric-oxyl Fe-III-O-center dot species) was found to occur on the quintet and septet surfaces. Then, conformational reorientation of the activated iron-oxygen ligand was found to be nearly thermoneutral with a barrier of ca. 50 W mol(-1). The final stage is the oxidative dealkylation of the damaged nucleobase with the rate-controlling step being the abstraction of a hydrogen atom from the damaging methyl group by the ferryloxo ligand. For this step, the calculated barrier of 87.4 kJ mol(-1) is in good agreement with the experimental activation energy of ca. 83 kJ mol(-1) for the enzyme-catalyzed reaction.