Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases
Activation and selectivity of OTUB-1 and OTUB-2 deubiquitinylases
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JNK信号的激活促进全反式视网膜诱导的小鼠感光细胞凋亡
DOI：
10.1074/jbc.ra120.013073
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发表时间：
2020-05-15
影响因子：
4.8
通讯作者：
Stein, Matthias
中科院分区：
文献类型：
--
作者：
Sivakumar, Dakshinamurthy;Kumar, Vikash;Stein, Matthias
卵巢肿瘤结构域 (OTU) 去泛素化半胱氨酸蛋白酶 OTUB1 和 OTUB2（OTU 泛素醛结合 1 和 2）是去泛素化酶 OTU 亚家族的代表性成员。去泛素化关键性地调节多种重要的细胞过程，例如细胞凋亡、细胞信号传导和生长。此外，在多种癌症中观察到 OTUB 表达升高，包括神经胶质瘤、子宫内膜癌、卵巢癌和乳腺癌。在这里，使用分子动力学模拟方法，我们发现 OTUB1 和 OTUB2 均表现出蛋白酶的催化三联体特征，但其构型和质子化状态不同。 OTUB1 蛋白具有预先安排的催化位点，活性位点残基 His(265) 和 Asp(267) 之间具有强静电相互作用。然而，在 OTUB2 中，催化三联体的排列是不同的。在没有泛素的情况下，OTUB2 中催化位点残基的中性状态更加稳定，导致这些残基之间的距离更大。只有在泛素结合后，OTUB2 中的催化三联体才会重新排列并使活性位点进入催化可行状态。对水通道的分析显示，OTUB1 的催化活性形式仅具有少数扩散轨迹，而在 OTUB2 中，催化位点是溶剂可接近的，并且大量的水分子到达并离开结合袋。有趣的是，在OTUB2中，催化残基His(224)和Asn(226)形成了稳定的氢键。我们提出，观察到的 OTUB1 和 OTUB2 之间在激活动力学、质子化状态、水通道和活性位点可及性方面的差异可能与 OTU 抑制剂的选择性设计相关。
The ovarian tumor domain (OTU) deubiquitinylating cysteine proteases OTUB1 and OTUB2 (OTU ubiquitin aldehyde binding 1 and 2) are representative members of the OTU subfamily of deubiquitinylases. Deubiquitinylation critically regulates a multitude of important cellular processes, such as apoptosis, cell signaling, and growth. Moreover, elevated OTUB expression has been observed in various cancers, including glioma, endometrial cancer, ovarian cancer, and breast cancer. Here, using molecular dynamics simulation approaches, we found that both OTUB1 and OTUB2 display a catalytic triad characteristic of proteases but differ in their configuration and protonation states. The OTUB1 protein had a prearranged catalytic site, with strong electrostatic interactions between the active-site residues His(265) and Asp(267). In OTUB2, however, the arrangement of the catalytic triad was different. In the absence of ubiquitin, the neutral states of the catalytic-site residues in OTUB2 were more stable, resulting in larger distances between these residues. Only upon ubiquitin binding did the catalytic triad in OTUB2 rearrange and bring the active site into a catalytically feasible state. An analysis of water access channels revealed only a few diffusion trajectories for the catalytically active form of OTUB1, whereas in OTUB2 the catalytic site was solvent-accessible, and a larger number of water molecules reached and left the binding pocket. Interestingly, in OTUB2, the catalytic residues His(224) and Asn(226) formed a stable hydrogen bond. We propose that the observed differences in activation kinetics, protonation states, water channels, and active-site accessibility between OTUB1 and OTUB2 may be relevant for the selective design of OTU inhibitors.