Crystal structure of the VapBC-15 complex from Mycobacterium tuberculosis reveals a two-metal ion dependent PIN-domain ribonuclease and a variable mode of toxin-antitoxin assembly
Crystal structure of the VapBC-15 complex from Mycobacterium tuberculosis reveals a two-metal ion dependent PIN-domain ribonuclease and a variable mode of toxin-antitoxin assembly
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DOI：
10.1016/j.jsb.2014.10.002
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发表时间：
2014-12-01
影响因子：
3
通讯作者：
Srinivasan, Alagiri
中科院分区：
文献类型：
--
作者：
Das, Uddipan;Pogenberg, Vivian;Srinivasan, Alagiri
虽然已知PIN(PILT N-末端)结构域蛋白具有核糖核酸酶活性，但其具体作用机制尚不清楚。VapCs形成一个核糖核酸酶家族，具有PIN结构域组装，被称为毒素。VAPB抗毒素可降低VapCs的活性。在这里，我们提出了来自结核分枝杆菌的VapBC-15毒素-抗毒素复合体的晶体结构，其分辨率为2.1埃。在晶体的每个不对称单元中，VAPB-15和VapC-15组分组装成一个杂四聚体(VAPB(2)C(2))和两个杂三聚体(VapBC(2))。VapC-15毒素的活性部位由一簇酸性氨基酸残基和两个二价金属离子组成，形成一个结构良好的核糖核酸酶活性部位。VapC-15毒素的催化残基分布与T4核糖核酸酶H和简氏甲烷球菌fen-1相似，这为这三种蛋白具有相似的活性机制提供了强有力的证据。VAPB(2)C(2)和VapBC(2)的存在强调了这样一个事实，即相同的抗毒素可以1：1和1：2的比例结合毒素。VapBC-15复合体的晶体结构测定首次揭示了PIN结构域核糖核酸酶蛋白，该蛋白在活性部位显示了两个金属离子，并显示了一种可变的毒素-抗毒素组装模式。该结构进一步表明，VAPB-15抗毒素结合在与假定底物结合的同一沟槽上，从而抑制VAPC-15‘S毒性。(C)2014 Elsevier Inc.保留所有权利。
Although PIN (PilT N-terminal)-domain proteins are known to have ribonuclease activity, their specific mechanism of action remains unknown. VapCs form a family of ribonucleases that possess a PIN-domain assembly and are known as toxins. The activities of VapCs are impaired by VapB antitoxins. Here we present the crystal structure of the VapBC-15 toxin-antitoxin complex from Mycobacterium tuberculosis determined to 2.1 angstrom resolution. The VapB-15 and VapC-15 components assemble into one heterotetramer (VapB(2)C(2)) and two heterotrimers (VapBC(2)) in each asymmetric unit of the crystal. The active site of VapC-15 toxin consists of a cluster of acidic amino acid residues and two divalent metal ions, forming a well organised ribonuclease active site. The distribution of the catalytic-site residues of the VapC-15 toxin is similar to that of T4 RNase H and of Methanococcus jannaschii FEN-1, providing strong evidence that these three proteins share a similar mechanism of activity. The presence of both VapB(2)C(2) and VapBC(2) emphasizes the fact that the same antitoxin can bind the toxin in 1:1 and 1:2 ratios. The crystal structure determination of the VapBC-15 complex reveals for the first time a PIN-domain ribonuclease protein that shows two metal ions at the active site and a variable mode of toxin-antitoxin assembly. The structure further shows that VapB-15 antitoxin binds to the same groove meant for the binding of putative substrate (RNA), resulting in the inhibition of VapC-15's toxicity. (C) 2014 Elsevier Inc. All rights reserved.