A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions.
A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions.
复制标题
DOI：
10.1021/ja103932d
复制
发表时间：
2010-07-14
影响因子：
15
通讯作者：
Zhang, Yingkai
中科院分区：
文献类型：
--
作者：
Wu, Ruibo;Wang, Shenglong;Zhou, Nengjie;Cao, Zexing;Zhang, Yingkai
锌依赖性组蛋白去乙酰化酶8 （HDAC8）催化组蛋白尾部乙酰基的去除，并在调节染色质结构和基因表达中起关键作用。其催化过程的详细知识非常重要，因为它已被确定为开发新的抗肿瘤药物的最有希望的靶点。通过Born-Oppenheimer从头计算QM/MM分子动力学模拟和伞式采样（一种最先进的模拟酶反应的方法），我们为最初提出的锌依赖性组蛋白去乙酰化酶的一般酸碱催化对机制提供了进一步的证据。相反，我们的研究结果表明，HDAC8采用质子穿梭催化机制，在初始决定速率的亲核攻击步骤中，中性的His143首先作为一般碱接受来自锌结合水分子的质子，然后将其穿梭到酰胺氮原子上，促进酰胺键的裂解。在脱乙酰过程中，Zn2+离子改变配位模式，发挥多重催化作用。对于K+离子，它位于催化Zn2+离子7 Å左右，在I类和II类hdac中保守，我们的模拟表明，它的去除会导致不同的过渡态结构和更高的自由能反应势场，从而决定速率步骤。发现这种保守K+离子的存在会增强底物结合，增加His143的碱度，增强锌离子的催化作用，提高酶环境对过渡态的稳定作用。
Zinc-dependent histone deacetylase 8 (HDAC8) catalyzes the removal of acetyl moieties from histone tails, and is critically involved in regulating chromatin structure and gene expression. The detailed knowledge of its catalytic process is of high importance since it has been established as a most promising target for the development of new anti-tumor drugs. By employing Born-Oppenheimer ab initio QM/MM molecular dynamics simulations and umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have provided further evidences against the originally proposed general acid-base catalytic pair mechanism for Zinc-dependent histone deacetylases. Instead, our results indicated that HDAC8 employs a proton-shuttle catalytic mechanism, in which a neutral His143 first serves as the general base to accept a proton from the zinc-bound water molecule in the initial rate-determining nucleophilic attack step, and then shuttles it to the amide nitrogen atom to facilitate the cleavage of the amide bond. During the deacetylation process, the Zn2+ ion changes its coordination mode and plays multiple catalytic roles. For the K+ ion, which is located about 7 Å from the catalytic Zn2+ ion and conserved in class I and II HDACs, our simulations indicated that its removal would lead to the different transition state structure and a higher free energy reaction barrier for the rate-determining step. It is found that the existence of this conserved K+ ion would enhance the substrate binding, increase the basicity of His143, strengthen the catalytic role of zinc ion and improve the transition state stabilization by the enzyme environment.
登录
查看更多内容
影响因子：
5.5
作者：
Blumberger, Jochen;Lamoureux, Guillaume;Klein, Michael L.
通讯作者：
Klein, Michael L.
影响因子：
14.8
作者：
Bradner, James E.;West, Nathan;Grachan, Melissa L.;Greenberg, Edward F.;Haggarty, Stephen J.;Warnow, Tandy;Mazitschek, Ralph
通讯作者：
Mazitschek, Ralph
影响因子：
64.8
作者：
Finnin, MS;Donigian, JR;Pavletich, NP
通讯作者：
Pavletich, NP
影响因子：
5.6
作者：
Gregoretti, IV;Lee, YM;Goodson, HV
通讯作者：
Goodson, HV
影响因子：
4.1
作者：
BEEMAN, D
通讯作者：
BEEMAN, D