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 Chem Theory Comput. 2019 Aug 13;15(8):4344-4350. doi: 10.1021/acs.jctc.8b01305. Epub 2019 Jul 18.
Uracil DNA glycosylase catalyzes the -glycosidic bond cleavage of uracil, thereby initiating the base excision repair mechanism for this DNA lesion. Here we employ hybrid quantum mechanics/molecular mechanics calculations to investigate the exact mechanism of the nucleophile attack and the role of the conserved His148 residue. Our calculations suggest that the C1'-N1 bond dissociation proceeds by a migration of the electrophilic sugar in the direction of the water nucleophile, resulting in a planar, oxocarbenium-like transition state. The subsequent nucleophile addition and proton transfer to a nearby base occur without a barrier. We assign the role of a proton acceptor to His148 and elucidate why mutations of this residue curtail the enzymatic activity but do not fully suppress it.
尿嘧啶 DNA 糖基化酶催化尿嘧啶的 -糖苷键断裂，从而启动该 DNA 损伤的碱基切除修复机制。在这里，我们采用杂化量子力学/分子力学计算来研究亲核攻击的确切机制和保守的 His148 残基的作用。我们的计算表明，C1'-N1 键的解离是通过带正电的糖在向水分子亲核试剂的方向迁移来进行的，导致平面的、类似氧杂碳正离子的过渡态。随后的亲核试剂添加和质子转移到附近的碱基上没有势垒。我们将 His148 的作用指定为质子受体，并阐明为什么该残基的突变会缩短酶的活性，但不会完全抑制它。
