Chair of Theoretical Chemistry, Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany.
Center for Integrated Protein Science Munich (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany.
J Phys Chem B. 2019 May 16;123(19):4173-4179. doi: 10.1021/acs.jpcb.8b11706. Epub 2019 May 1.
Thymine DNA glycosylase (TDG) initiates the base excision repair mechanism for the deamination and oxidation products of cytosine and 5-methylcytosine. This enzyme has a key role in epigenetic regulation, and its catalytic inactivation results in, e.g., mice embryo lethality. Here, we employ molecular dynamics simulations and quantum mechanics/molecular mechanics calculations to investigate the reaction mechanism of the TDG-catalyzed N-glycosidic bond hydrolysis of the modified base 5-formylcytosine. Our results reveal a reaction pathway, which in its first step features a reorganization of the substrate that lowers the barrier height for the subsequent C1'-N1 bond dissociation. The suggested mechanism is consistent with the experimental data, as it is not acid-catalyzed and proceeds through an oxocarbenium-like transition state. It also provides insights into the catalytic roles of the Thr197 and Asn140 residues.
胸腺嘧啶 DNA 糖基化酶（TDG）启动碱基切除修复机制，以修复胞嘧啶和 5-甲基胞嘧啶的脱氨和氧化产物。该酶在表观遗传调控中发挥着关键作用，其催化失活会导致例如小鼠胚胎致死。在这里，我们采用分子动力学模拟和量子力学/分子力学计算来研究 TDG 催化的修饰碱基 5-甲醛胞嘧啶的 N-糖苷键水解反应的机制。我们的结果揭示了一条反应途径，其中第一步涉及底物的重排，降低了后续 C1'-N1 键解离的势垒高度。所提出的机制与实验数据一致，因为它不是酸催化的，而是通过氧杂碳正离子样过渡态进行的。它还深入了解了 Thr197 和 Asn140 残基的催化作用。
