A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate
A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate
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DOI：
10.1021/acs.biochem.5b00396
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发表时间：
2015-07-14
期刊：
影响因子：
2.9
通讯作者：
Webster, Charles Edwin
中科院分区：
文献类型：
--
作者：
DeYonker, Nathan J.;Webster, Charles Edwin
酪氨酸-DNA磷酸二酯酶I（Tdp 1）是一种在真核生物中保守的DNA修复酶，其催化拓扑异构酶I的酪氨酸残基与DNA的3 '-磷酸之间的磷酸二酯键的水解。原子水平的细节Tdp 1的机制提出和分析使用一个完全量子力学，几何约束模型。计算模型的结构基础是人Tdp 1（hTdp 1，蛋白质数据库条目1 RFF）的钒酸盐抑制晶体结构。密度泛函理论计算用于获得热力学和动力学数据沿着的催化途径，包括磷酰基转移和随后的水解。位于过渡态和中间体沿着反应坐标建议与五配位膦中间体的缔合磷酰基转移机制。与磷脂酶D的理论和实验结果类似，hTdp 1的拟议机制也包括四配位磷酸组氨酸“死端”产物的化学上有利的可能性。
Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.