Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations.
Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations.
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DOI：
10.1021/ct500572t
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发表时间：
2014-11-11
影响因子：
5.5
通讯作者：
Cisneros, G. Andres
中科院分区：
文献类型：
--
作者：
Fang, Dong;Cisneros, G. Andres
AlkB是DNA脱烷基酶家族的标题酶，其催化核碱基的直接氧化脱烷基化。在形成FeIV-氧代后，AlkB催化N1-甲基腺嘌呤（1-meA）脱烷基化的常规机理包括氧代部分的重新取向、氢提取、OH从Fe原子反弹到甲基加合物以及所得甲醇盐的解离以获得修复的腺嘌呤碱和甲醛。另一种途径与氢氧化物作为一个配体结合到铁原子的建议和研究QM/MM模拟。结果表明，OH-对吸氢和OH反弹的势垒影响不大。详细讨论了酶和OH-配体对FeIV-氧代部分的氢提取的影响。新的OH反弹步骤与质子转移到OH-配体相结合，并产生新的两性离子中间体。这种两性结构也可以表征为Fe-O-C络合物，并促进甲醛的形成。相比之下，对于H2O与铁结合的途径，OH反弹步骤的羟基产物首先需要在将质子转移到Glu 136或其他残基/底物之前与金属中心解结合。我们的理论结果和实验结果之间的一致性进行了讨论。本研究为非血红素FeII和α-酮戊二酸（α-KG）依赖性双加氧酶的DNA氧化修复机制提供了新的见解，并为AlkB的底物偏好性提供了可能的解释。
AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N1-methyl adenine (1-meA) catalyzed by AlkB after the formation of FeIV–oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH– has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH– ligand on the hydrogen abstraction by the FeIV–oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH– ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe–O–C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H2O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme FeII and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB.
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影响因子：
5.5
作者：
Contreras-Garcia, Julia;Johnson, Erin R.;Keinan, Shahar;Chaudret, Robin;Piquemal, Jean-Philip;Beratan, David N.;Yang, Weitao
通讯作者：
Yang, Weitao
影响因子：
1.7
作者：
Fang, Dong;Piquemal, Jean-Philip;Cisneros, G. Andres
通讯作者：
Cisneros, G. Andres
影响因子：
15
作者：
Hirao, H;Kumar, D;Shaik, S
通讯作者：
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影响因子：
4.3
作者：
Bellow, James A.;Fang, Dong;Groysman, Stanislav
通讯作者：
Groysman, Stanislav
影响因子：
3.3
作者：
Liu, Haining;Llano, Jorge;Gauld, James W.
通讯作者：
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