The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation.
The mechanism of ubiquitination in the cullin-RING E3 ligase machinery: conformational control of substrate orientation.
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Cullin环E3连接酶机械中泛素化的机制：底物方向的构象控制。
DOI：
10.1371/journal.pcbi.1000527
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发表时间：
2009-10
影响因子：
4.3
通讯作者：
Nussinov R
中科院分区：
文献类型：
--
作者：
Liu J;Nussinov R
在cullin-RING E3泛素连接酶中，底物结合蛋白，如VHL盒、SOCS盒或F盒蛋白，募集底物用于泛素化，精确定位和定向底物用于泛素转移。然而，E3机器如何精确定位基板是未知的。在这里，我们模拟了9种底物结合蛋白：Skp 2、Fbw 7、β-TrCP 1、Cdc 4、Fbs 1、TIR 1、pVHL、SOCS 2和SOCS 4，它们以未结合的形式与Skp 1、ASK 1或Elongin C结合。所有九种蛋白质都有两个结构域：一个与底物结合;另一个与E3连接酶模块Skp 1/ASK 1/Elongin C结合。我们发现，在所有情况下，灵活的域间连接器作为铰链，旋转底物结合域，最佳和准确地定位它的泛素转移。我们观察到一个保守的脯氨酸在所有九个蛋白质的接头。在所有的情况下，脯氨酸基本上折叠，并且折叠与骨架向E2/泛素的旋转有关。我们进一步观察到，接头的灵活性可以通过与任一结构域相关的结合事件进行变构调节。我们的结论是，灵活的接头在底物结合蛋白定位底物的泛素转移。我们的研究结果提供了一个机制，泛素化和聚泛素化，说明这些过程是在构象控制。泛素-蛋白酶体系统通过几个步骤调节蛋白质降解。cullin-RING E3连接酶机制参与其中之一。在这一步中，泛素从E2转移到底物蛋白，标记底物蛋白进行降解。然而，当E3，E3-底物和E2-泛素晶体结构一起建模时，泛素化的E2和底物结合位点之间的距离是1050 - 59 μ m，提出了E3机制如何桥接距离并定向底物以进行泛素转移的问题。我们进行了明确的溶剂模拟的PDB中的所有九个可用的底物结合蛋白质复合物，有和没有相应的E3组件，它们被绑定。在所有这九个底物结合蛋白中，我们注意到一个灵活的接头，它在很大程度上以相同的方向旋转底物结合结构域，朝向E2-泛素。我们进一步注意到，与任一结构域相关的结合事件对柔性进行变构调节。结果表明，柔性接头作为铰链旋转底物结合结构域，并准确定位底物的泛素化。因此，这些模拟为机器如何操作以定向底物进行泛素化的问题提供了答案。
In cullin-RING E3 ubiquitin ligases, substrate binding proteins, such as VHL-box, SOCS-box or the F-box proteins, recruit substrates for ubiquitination, accurately positioning and orienting the substrates for ubiquitin transfer. Yet, how the E3 machinery precisely positions the substrate is unknown. Here, we simulated nine substrate binding proteins: Skp2, Fbw7, β-TrCP1, Cdc4, Fbs1, TIR1, pVHL, SOCS2, and SOCS4, in the unbound form and bound to Skp1, ASK1 or Elongin C. All nine proteins have two domains: one binds to the substrate; the other to E3 ligase modules Skp1/ASK1/Elongin C. We discovered that in all cases the flexible inter-domain linker serves as a hinge, rotating the substrate binding domain, optimally and accurately positioning it for ubiquitin transfer. We observed a conserved proline in the linker of all nine proteins. In all cases, the prolines pucker substantially and the pucker is associated with the backbone rotation toward the E2/ubiquitin. We further observed that the linker flexibility could be regulated allosterically by binding events associated with either domain. We conclude that the flexible linker in the substrate binding proteins orients the substrate for the ubiquitin transfer. Our findings provide a mechanism for ubiquitination and polyubiquitination, illustrating that these processes are under conformational control. The Ubiquitin-Proteasome System regulates protein degradation via several steps. The cullin-RING E3 ligase machinery is involved in one of these. In this step, ubiquitin is transferred from E2 to the substrate protein, labeling the substrate protein for degradation. However, when E3, E3-substrate and E2-ubiquitin crystal structures are modeled together, the distance between ubiquitinated E2 and the substrate binding site is ∼50–59Å, raising the question how the E3 machinery bridges the distance and orients the substrate for the ubiquitin transfer. We performed explicit solvent simulations for all nine available substrate binding protein complexes in the PDB, with and without the corresponding E3 components to which they are bound. In all of these nine substrate binding proteins, we noticed a flexible linker that rotates the substrate binding domain to a great extent in the same direction, toward the E2-ubiquin. We further noticed that the flexibility is regulated allosterically by binding events associated with either domain. The results suggest that the flexible linker serves as a hinge to rotate the substrate binding domain and to accurately position the substrate for ubiquitination. As such, the simulations suggest an answer to the question of how the machinery operates to orient the substrate for ubiquitination.
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影响因子：
64.5
作者：
Duda, David M.;Borg, Laura A.;Scott, Daniel C.;Hunt, Harold W.;Hammel, Michal;Schulman, Brenda A.
通讯作者：
Schulman, Brenda A.
影响因子：
16
作者：
Hao, B;Zheng, N;Pavletich, NP
通讯作者：
Pavletich, NP
影响因子：
16
作者：
Hao, Bing;Oehlmann, Stephanie;Pavletich, Nikola P.
通讯作者：
Pavletich, Nikola P.
DOI：
10.1073/pnas.0601638103
发表时间：
2006-05-16
影响因子：
11.1
作者：
Bullock, Alex N.;Debreczeni, Judit E.;Knapp, Stefan
通讯作者：
Knapp, Stefan
影响因子：
2.9
作者：
Hayward, S;Lee, RA
通讯作者：
Lee, RA