1Department of Biochemistry, University of Toronto, Toronto, Ontario M5G 1M1 Canada.
2Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8 Canada.
Commun Biol. 2019 Nov 13;2:410. doi: 10.1038/s42003-019-0656-3. eCollection 2019.
Bacterial ClpP is a highly conserved, cylindrical, self-compartmentalizing serine protease required for maintaining cellular proteostasis. Small molecule acyldepsipeptides (ADEPs) and activators of self-compartmentalized proteases 1 (ACP1s) cause dysregulation and activation of ClpP, leading to bacterial cell death, highlighting their potential use as novel antibiotics. Structural changes in and ClpP upon binding to novel ACP1 and ADEP analogs were probed by X-ray crystallography, methyl-TROSY NMR, and small angle X-ray scattering. ACP1 and ADEP induce distinct conformational changes in the ClpP structure. However, reorganization of electrostatic interaction networks at the ClpP entrance pores is necessary and sufficient for activation. Further activation is achieved by formation of ordered N-terminal axial loops and reduction in the structural heterogeneity of the ClpP cylinder. Activating mutations recapitulate the structural effects of small molecule activator binding. Our data, together with previous findings, provide a structural basis for a unified mechanism of compound-based ClpP activation.
细菌 ClpP 是一种高度保守的圆柱形自分隔丝氨酸蛋白酶，对于维持细胞内蛋白质稳态至关重要。小分子酰基二肽（ADEPs）和自分隔蛋白酶 1（ACP1）激活剂可导致 ClpP 失调和激活，从而导致细菌细胞死亡，这凸显了它们作为新型抗生素的潜在用途。通过 X 射线晶体学、甲基-TROSY NMR 和小角度 X 射线散射研究了与新型 ACP1 和 ADEP 类似物结合时 ClpP 的结构变化。ACP1 和 ADEP 诱导 ClpP 结构的独特构象变化。然而，ClpP 入口孔处静电相互作用网络的重新组织对于激活是必需且充分的。通过形成有序的 N 端轴向环和降低 ClpP 圆柱的结构异质性进一步实现激活。激活突变再现了小分子激活剂结合的结构效应。我们的数据与以前的发现一起，为基于化合物的 ClpP 激活的统一机制提供了结构基础。
