The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea-based inhibitor
The molecular structure of epoxide hydrolase B from Mycobacterium tuberculosis and its complex with a urea-based inhibitor
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DOI：
10.1016/j.jmb.2008.06.030
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发表时间：
2008-09-12
影响因子：
5.6
通讯作者：
James, Michael N. G.
中科院分区：
文献类型：
--
作者：
Biswal, Bichitra K.;Morisseau, Christophe;James, Michael N. G.
结核分枝杆菌（Mycobacterium tuberculosis，Mtb）是主要感染巨噬细胞的细胞内病原体，是人类感染性疾病结核病的病原体。Mtb基因组编码至少六种环氧化物水解酶（EH A至F）。EH将环氧化物转化为反式二氢二醇，并在药物代谢以及信号分子的加工中发挥作用。在此，我们报告了未结合的Mtb EHB和Mtb EHB结合到pc帐篷，低纳摩尔（IC（50）约为19 nM）尿素为基础的抑制剂的晶体结构，分别在2.1和2.4埃的分辨率。该酶是一种同二聚体，每个单体采用经典的α/β水解酶折叠，组成催化结构域;有一个帽结构域，调节进入活性位点。包含Asp 104、His 333和Asp 302的催化三联体从催化结构域突出到两个结构域之间的底物结合腔中。抑制剂的脲部分结合在催化空腔中，部分模仿底物结合;两个脲氮原子向AsP 104的亲核羧酸酯提供氢键，脲部分的羰基氧从Tyr 164和Tyr 272的酚氧原子接收氢键。这两个残基的酚氧基团在环氧化物水解裂解期间提供亲电辅助。在抑制剂结合后，结合位点残基经历微妙的结构重排。特别地，Ile 137的侧链围绕其C（alpha）-C（beta）键显示出约1.20度的旋转，以容纳抑制剂。这些发现不仅阐明了酶的机制，而且为开发对所有α/β型Mtb EH具有良好药代动力学特征的强效抑制剂开辟了道路。(C)2008爱思唯尔有限公司版权所有。
Mycobacterium tuberculosis (Mtb), the intracellular pathogen that infects macrophages primarily, is the causative agent of the infectious disease tuberculosis in humans. The Mtb genome encodes at least six epoxide hydrolases (EHs A to F). EHs convert epoxides to trans-dihydrodiols and have roles in drug metabolism as well as in the processing of signaling molecules. Herein, we report the crystal structures of unbound Mtb EHB and Mtb EHB bound to a pc tent, low-nanomolar (IC(50) approximate to 19 nM) urea-based inhibitor at 2.1 and 2.4 angstrom resolution, respectively. The enzyme is a homodimer, each monomer adopts the classical alpha/beta hydrolase fold that composes the catalytic domain; there is a cap domain that regulates access to the active site. The catalytic triad, comprising Asp104, His333 and Asp302, protrudes from the catalytic domain into the substrate binding cavity between the two domains. The urea portion of the inhibitor is bound in the catalytic cavity, mimicking, in part, the substrate binding; the two Urea nitrogen atoms donate hydrogen bonds to the nucleophilic carboxylate of AsP104, and the carbonyl oxygen of the urea moiety receives hydrogen bonds from the phenolic oxygen atoms of Tyr164 and Tyr272. The phenolic oxygen groups of these two residues provide electrophilic assistance during the epoxide hydrolytic cleavage. Upon inhibitor binding, the binding-site residues undergo subtle structural rearrangement. In particular, the side chain of Ile137 exhibits a rotation of around 1.20 degrees about its C(alpha)-C(beta) bond in order to accommodate the inhibitor. These findings have not only shed light on the enzyme mechanism but also have opened a path for the development of potent inhibitors with good pharmacokinetic profiles against all Mtb EHs of the alpha/beta type. (C) 2008 Elsevier Ltd. All rights reserved.