Crystallographic structure of the nuclease domain of 3′hExo, a DEDDh family member, bound to rAMP
Crystallographic structure of the nuclease domain of 3′hExo, a DEDDh family member, bound to rAMP
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DOI：
10.1016/j.jmb.2004.08.055
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发表时间：
2004-10-15
影响因子：
5.6
通讯作者：
Patel, DJ
中科院分区：
文献类型：
--
作者：
Cheng, Y;Patel, DJ
最近已经鉴定出人3 '-5'-核糖核酸外切酶（3 'hExo），并且显示其负责组蛋白mRNA降解。在功能上，3 'hExo和茎环结合蛋白（SLBP）靶向独特的高度保守的茎环RNA支架的相对面朝向组蛋白mRNA的3'端，其由6 bp茎和4 nt环组成，随后是ACCCA序列。它的秀丽隐杆线虫同源物ERI-1已被证明在体外降解小干扰RNA，并在神经元细胞中作为RNA干扰的负调节剂发挥作用。我们已经在1.6埃分辨率下确定了在Mg 2+存在下与rAMP复合的3 'hExo的核酸酶结构域（Nuc）的结构。Nuc结构域采用α/β球状折叠，其中四个酸性残基在活性位点内协调双核金属簇，其拓扑结构与DEDDh核酸外切酶家族成员相关，尽管一级序列同一性水平非常低。Nuc活性位点中的两个镁阳离子与D134、E136、D234和D298配位，并且与H293一起，其可以潜在地充当通用碱基，提供在3 '->5'方向上水解切割结合的RNA的平台。结合的rAMP位于深活性位点口袋内，其嘌呤环与疏水性F185和L189侧链紧密堆积，其糖2 '-OH和3'-OH基团与Nuc的骨架原子氢键合。Nuc和epsilon 186（大肠杆菌DNA聚合酶III校对结构域）的活性位点之间存在惊人的相似性，分别为RNA降解和DNA编辑提供了共同的水解切割机制。(C)2004爱思唯尔有限公司保留所有权利。
A human 3'-5'-exoribonuclease (3'hExo) has recently been identified and shown to be responsible for histone mRNA degradation. Functionally, 3'hExo and a stem-loop binding protein (SLBP) target opposite faces of a unique highly conserved stem-loop RNA scaffold towards the 3' end of histone mRNA, which is composed of a 6 bp stem and a 4 nt loop, followed by an ACCCA sequence. Its Caenorhabditis elegans homologue, ERI-1, has been shown to degrade small interfering RNA in vitro and to function as a negative regulator of RNA interference in neuronal cells. We have determined the structure of the nuclease domain (Nuc) of 3'hExo complexed with rAMP in the presence of Mg2+ at 1.6 Angstrom resolution. The Nuc domain adopts an alpha/beta globular fold, with four acidic residues coordinating a binuclear metal cluster within the active site, whose topology is related to DEDDh exonuclease family members, despite a very low level of primary sequence identity. The two magnesium cations in the Nuc active site are coordinated to D134, E136, D234 and D298, and together with H293, which can potentially act as a general base, provide a platform for hydrolytic cleavage of bound RNA in the 3'-->5' direction. The bound rAMP is positioned within a deep active-site pocket, with its purine ring close-packed with the hydrophobic F185 and L189 side-chains and its sugar 2'-OH and 3'-OH groups hydrogen bonded to backbone atoms of Nuc. There are striking similarities between the active sites of Nuc and epsilon186, an Escherichia coli DNA polymerase III proofreading domain, providing a common hydrolytic cleavage mechanism for RNA degradation and DNA editing, respectively. (C) 2004 Elsevier Ltd. All rights reserved.