Complex structure of OspI and Ubc13: the molecular basis of Ubc13 deamidation and convergence of bacterial and host E2 recognition.
Complex structure of OspI and Ubc13: the molecular basis of Ubc13 deamidation and convergence of bacterial and host E2 recognition.
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OspI和Ubc13的复杂结构：Ubc13脱酰胺的分子基础以及细菌和宿主E2识别的趋同
DOI：
10.1371/journal.ppat.1003322
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发表时间：
2013
期刊：
影响因子：
6.7
通讯作者：
Zhu Y
中科院分区：
文献类型：
--
作者：
Fu P;Zhang X;Jin M;Xu L;Wang C;Xia Z;Zhu Y
Ubc13是NF-κB信号通路中一个重要的泛素偶联（E2）酶。志贺氏菌效应物OspI靶向Ubc13并将Ubc13的Gln100脱酰胺为谷氨酸残基，从而抑制宿主炎症反应。在这里，我们以2.3 Å分辨率报道了OspI-Ubc13配合物的晶体结构。该结构揭示了OspI利用两个不同的电荷区与Ubc13的α1螺旋、L1环和L2环广泛相互作用。Gln100残基结合在OspI的亲水催化口袋内。对比Ubc13结合与野生型自由OspI结构发现，Ubc13结合诱导了催化袋的显著结构重组，提示底物结合可能参与了OspI的催化作用。Ubc13中的ospi结合位点与宿主泛素E3连接酶和去泛素化酶的结合残基大部分重叠，这表明细菌效应蛋白和宿主蛋白利用Ubc13上的同一表面进行特异性识别。生化结果表明，OspI中两个不同的带电荷区域对于与Ubc13的相互作用都很重要，并且Ubc13中识别OspI的特异性决定因素存在于α1螺旋和L2区域的不同残基中。我们的研究揭示了OspI对Ubc13脱酰胺的分子基础，以及细菌和宿主蛋白对E2识别的趋同。革兰氏阴性致病菌志贺氏菌感染人肠上皮细胞并引起严重的炎症性结肠炎（细菌性痢疾）。志贺氏菌携带约220 kb的毒力质粒，编码III型分泌系统（T3SS）蛋白分泌装置和许多效应蛋白。志贺氏菌利用T3SS将效应蛋白传递到宿主细胞中，靶向关键信号分子，操纵宿主生理过程，从而促进感染和增殖。OspI是一种新发现的志贺氏菌效应物，靶向宿主Ubc13蛋白，这是NF-κB信号通路中一个关键的泛素结合酶。OspI将Ubc13的Gln100脱酰胺为谷氨酸残基，从而破坏traf6催化的多泛素化并抑制宿主的炎症反应。然而，这种特殊脱酰胺的结构机制尚不清楚。通过晶体学，我们确定了OspI-Ubc13配合物的结构。该结构说明了OspI如何与Ubc13相互作用，以及Ubc13如何诱导OspI的构象变化。结合结构分析和生化分析，我们揭示了OspI如何区分Ubc13与其他泛素偶联酶，并发现OspI与宿主TRAF6、CHIP和OTUB1结合在Ubc13的相同表面区域。我们的研究揭示了OspI对Ubc13脱酰胺的分子机制，并为细菌和宿主蛋白对E2的识别提供了新的见解。
Ubc13 is an important ubiquitin-conjugating (E2) enzyme in the NF-κB signaling pathway. The Shigella effector OspI targets Ubc13 and deamidates Gln100 of Ubc13 to a glutamic acid residue, leading to the inhibition of host inflammatory responses. Here we report the crystal structure of the OspI-Ubc13 complex at 2.3 Å resolution. The structure reveals that OspI uses two differently charged regions to extensively interact with the α1 helix, L1 loop and L2 loop of Ubc13. The Gln100 residue is bound within the hydrophilic catalytic pocket of OspI. A comparison between Ubc13-bound and wild-type free OspI structures revealed that Ubc13 binding induces notable structural reassembly of the catalytic pocket, suggesting that substrate binding might be involved in the catalysis of OspI. The OspI-binding sites in Ubc13 largely overlap with the binding residues for host ubiquitin E3 ligases and a deubiquitinating enzyme, which suggests that the bacterial effector and host proteins exploit the same surface on Ubc13 for specific recognition. Biochemical results indicate that both of the differently charged regions in OspI are important for the interaction with Ubc13, and the specificity determinants in Ubc13 for OspI recognition reside in the distinct residues in the α1 helix and L2 region. Our study reveals the molecular basis of Ubc13 deamidation by OspI, as well as a convergence of E2 recognition by bacterial and host proteins. The Gram-negative pathogenic bacterium Shigella infects human intestinal epithelium cells and causes severe inflammatory colitis (bacillary dysentery). Shigella harbors an approximately 220-kb virulence plasmid that encodes a type III secretion system (T3SS) protein secretion apparatus and many effector proteins. Using the T3SS, Shigella delivers the effector proteins into the host cells, targeting key signal molecules and manipulating the host physiological processes and thereby promoting infection and multiplication. OspI, a newly identified Shigella effector, targets the host Ubc13 protein, a critical ubiquitin-conjugating enzyme in the NF-κB signaling pathway. OspI deamidates Gln100 of Ubc13 to a glutamic acid residue, thereby disrupting TRAF6-catalyzed polyubiquitination and dampening host inflammatory responses. However, the structural mechanism of this specific deamidation is unclear. Through crystallography, we have determined the structure of the OspI-Ubc13 complex. The structure illustrates how OspI interacts with Ubc13 and how Ubc13 induces conformational changes in OspI. Combining structural analysis and biochemical assays, we revealed how OspI distinguishes Ubc13 from other ubiquitin conjugating enzymes and found that OspI binds to the same surface region on Ubc13 as host TRAF6, CHIP and OTUB1. Our study sheds light on the molecular mechanism of Ubc13 deamidation by OspI and provides new insights into E2 recognition by bacterial and host proteins.
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影响因子：
5.6
作者：
Hsu, Yun;Jubelin, Gregory;Taieb, Frederic;Nougayrede, Jean-Philippe;Oswald, Eric;Stebbins, C. Erec
通讯作者：
Stebbins, C. Erec
影响因子：
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作者：
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通讯作者：
Peeters, Nemo
DOI：
10.1107/s0907444904019158
发表时间：
2004-12-01
影响因子：
2.2
作者：
Emsley, P;Cowtan, K
通讯作者：
Cowtan, K
影响因子：
64.5
作者：
Dong, Na;Zhu, Yongqun;Shao, Feng
通讯作者：
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影响因子：
3.9
作者：
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通讯作者：
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