Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris
Theoretical Study of the Catalytic Mechanism of DNA-(N4-Cytosine)-Methyltransferase from the Bacterium Proteus vulgaris
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DOI：
10.1021/jp911036w
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发表时间：
2010-07-01
影响因子：
3.3
通讯作者：
Tunon, Inaki
中科院分区：
文献类型：
--
作者：
Aranda, Juan;Roca, Maite;Tunon, Inaki
本文用量子力学/分子力学（QM/MM）混合方法研究了M.PvuII催化的环外N_4位胞嘧啶甲基化反应机理。通过在酶的活性位点放置单个胞嘧啶碱基来制备反应模型。在该模型中，碱基的环外氨基与Ser 53的羟基氧原子和Pro 54的羰基氧原子建立氢键相互作用。该反应机制涉及从Ado Met到N4原子的直接甲基转移和从该原子到Ser 53的质子转移，Ser 53又将质子转移到Asp 96。在AM 1/MM和B3 LYP/MM水平上探索了质子转移和甲基化步骤的不同时间，包括固定结构的定位和表征。在我们的最佳估计下，反应通过同时但异步的质子转移从Ser 53到Asp 96和从胞嘧啶的N4到Ser 53，然后通过从Ado Met到胞嘧啶的环外N4的直接甲基转移进行。
In this paper the reaction mechanism for methylation of cytosine at the exocyclic N4 position catalyzed by M.PvuII has been explored by means of hybrid quantum mechanics/molecular mechanics (QM/MM) methods. A reaction model was prepared by placing a single cytosine base in the active site of the enzyme. In this model the exocyclic amino group of the base establishes hydrogen bond interactions with the hydroxyl oxygen atom of Ser53 and the carbonyl oxygen atom of Pro54. The reaction mechanism involves a direct methyl transfer from Ado Met to the N4 atom and a proton transfer from this atom to Ser53, which in turn transfers a proton to Asp96. Different timings for the proton transfers and methylation steps have been explored at the AM1/MM and B3LYP/MM levels including localization and characterization of stationary structures. At our best estimate the reaction proceeds by means of a simultaneous but asynchronous proton transfer from Ser53 to Asp96 and from N4 of cytosine to Ser53 followed by a direct methyl transfer from Ado Met to the exocyclic N4 of cytosine.