Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA.
Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany.
Nat Commun. 2022 Feb 11;13(1):838. doi: 10.1038/s41467-022-28186-y.
The proteasome recognizes ubiquitinated proteins and can also edit ubiquitin marks, allowing substrates to be rejected based on ubiquitin chain topology. In yeast, editing is mediated by deubiquitinating enzyme Ubp6. The proteasome activates Ubp6, whereas Ubp6 inhibits the proteasome through deubiquitination and a noncatalytic effect. Here, we report cryo-EM structures of the proteasome bound to Ubp6, based on which we identify mutants in Ubp6 and proteasome subunit Rpt1 that abrogate Ubp6 activation. The Ubp6 mutations define a conserved region that we term the ILR element. The ILR is found within the BL1 loop, which obstructs the catalytic groove in free Ubp6. Rpt1-ILR interaction opens the groove by rearranging not only BL1 but also a previously undescribed network of three interconnected active-site-blocking loops. Ubp6 activation and noncatalytic proteasome inhibition are linked in that they are eliminated by the same mutations. Ubp6 and ubiquitin together drive proteasomes into a unique conformation associated with proteasome inhibition. Thus, a multicomponent allosteric switch exerts simultaneous control over both Ubp6 and the proteasome.
蛋白酶体识别泛素化的蛋白质，也可以编辑泛素标记，允许根据泛素链拓扑结构拒绝底物。在酵母中，编辑由去泛素化酶 Ubp6 介导。蛋白酶体激活 Ubp6，而 Ubp6 通过去泛素化和非催化作用抑制蛋白酶体。在这里，我们报告了基于结合 Ubp6 的蛋白酶体的冷冻电镜结构，根据这些结构，我们鉴定了 Ubp6 和蛋白酶体亚基 Rpt1 中的突变体，这些突变体消除了 Ubp6 的激活。Ubp6 突变定义了一个保守区域，我们称之为 ILR 元件。ILR 位于 BL1 环内，该环在游离 Ubp6 中阻碍催化槽。Rpt1-ILR 相互作用通过不仅重新排列 BL1 而且重新排列以前未描述的三个相互连接的活性位点阻断环网络来打开槽。Ubp6 的激活和非催化蛋白酶体抑制是相关的，因为它们被相同的突变消除。Ubp6 和泛素一起将蛋白酶体驱动到与蛋白酶体抑制相关的独特构象。因此，多组分变构开关对 Ubp6 和蛋白酶体同时进行控制。
