Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination.
Flexible cullins in cullin-RING E3 ligases allosterically regulate ubiquitination.
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DOI：
10.1074/jbc.m111.277236
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发表时间：
2011-11-25
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影响因子：
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通讯作者：
Nussinov R
中科院分区：
文献类型：
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作者：
Liu J;Nussinov R
背景：蛋白质泛素化调节关键的生物学过程，包括功能不全的蛋白质的降解。结果：1、4A、5号库不是刚性的。它们都是具有构象状态优先分布的柔性支架。结论：cullin的灵活性是以变构方式调节的，允许cullin环E3泛素连接酶将E2底物距离增加到特定范围，从而促进多泛素化。意义：库林不是惰性的支架，它通过变构来调节泛素化。具有保守结构的库林斯如何适应形状和大小不同的底物结合蛋白？库林环E3泛素连接酶促进泛素从E2转移到底物，标记底物进行降解。它们含有底物结合蛋白、接头蛋白、cullin蛋白和RBX蛋白。此前，我们已经证明底物结合和RBX蛋白是灵活的。这允许缩短启动泛素化的E2-底物距离或增加距离以适应多泛素链。然而，扑杀的作用仍不清楚。Cullin是一种刚性支架，还是一种灵活的、积极协助泛素转移反应的支架？为什么有不同的库林，这些库林是如何特别促进不同底物的泛素化的？为了回答这些问题，我们基于Cul1、Cul4A和Cul5的晶体结构进行了结构分析和分子动力学模拟。我们的结果表明，这三种库林支架不是刚性支架，但在N-末端区域是具有保守铰链的柔性支架。然而，不同的库林人之间的灵活性程度是不同的。有趣的是，Cul1的灵活性也可以通过删除N-末端结构域中的长环(在Cul4A中不存在)来改变，这表明该环可能具有变构功能作用。在所有三种情况下，这些构象变化都将E2-底物距离增加到特定范围，以促进多泛素化，这表明库林斯不是惰性支架蛋白，而是变构调节泛素化。
Background: Protein ubiquitination regulates critical biological processes, including degradation of malfunctioning proteins. Results: We show that Cul1, Cul4A, and Cul5 are not rigid. All are flexible scaffolds with preferred distributions of conformational states. Conclusion: Cullin flexibilities are regulated allosterically, allowing the cullin-RING E3 ubiquitin ligases to increase the E2-substrate distance to a specific range, facilitating polyubiquitination. Significance: Cullins are not inert scaffolds and allosterically regulate ubiquitination. How do the cullins, with conserved structures, accommodate substrate-binding proteins with distinct shapes and sizes? Cullin-RING E3 ubiquitin ligases facilitate ubiquitin transfer from E2 to the substrate, tagging the substrate for degradation. They contain substrate-binding, adaptor, cullin, and Rbx proteins. Previously, we showed that substrate-binding and Rbx proteins are flexible. This allows shortening of the E2-substrate distance for initiation of ubiquitination or increasing the distance to accommodate the polyubiquitin chain. However, the role of the cullin remained unclear. Is cullin a rigid scaffold, or is it flexible and actively assists in the ubiquitin transfer reaction? Why are there different cullins, and how do these cullins specifically facilitate ubiquitination for different substrates? To answer these questions, we performed structural analysis and molecular dynamics simulations based on Cul1, Cul4A, and Cul5 crystal structures. Our results show that these three cullins are not rigid scaffolds but are flexible with conserved hinges in the N-terminal domain. However, the degrees of flexibilities are distinct among the different cullins. Of interest, Cul1 flexibility can also be changed by deletion of the long loop (which is absent in Cul4A) in the N-terminal domain, suggesting that the loop may have an allosteric functional role. In all three cases, these conformational changes increase the E2-substrate distance to a specific range to facilitate polyubiquitination, suggesting that rather than being inert scaffold proteins, cullins allosterically regulate ubiquitination.