Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase
Multi-state structure determination and dynamics analysis reveals a new ubiquitin-recognition mechanism in yeast ubiquitin C-terminal hydrolase
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DOI：
10.1101/2021.04.22.440356
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发表时间：
2021-04
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通讯作者：
Mayu Okada;Yu Tateishi;Eri Nojiri;T. Mikawa;S. Rajesh;Hiroki Ogasa;Takumi Ueda;H. Yagi;T. Kohno;T. Kigawa;I. Shimada;P. Güntert;Yutaka Ito;T. Ikeya
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作者：
Mayu Okada;Yu Tateishi;Eri Nojiri;T. Mikawa;S. Rajesh;Hiroki Ogasa;Takumi Ueda;H. Yagi;T. Kohno;T. Kigawa;I. Shimada;P. Güntert;Yutaka Ito;T. Ikeya
尽管越来越多的证据表明，蛋白质动力学是必不可少的了解生物活性的结构基础，它仍然具有挑战性的可视化的动态空间描述，并与其分子功能的瞬时构象。我们已经开发了一种新的NMR蛋白质结构测定方法，使用多种类型的NMR数据，包括顺磁NMR和残余偶极耦合，以及传统的NOE推断多态构象。将这些数据整合到结构计算中可以描绘生物大分子的准确系综结构。将该方法应用于蛋白质酵母泛素水解酶1（YUH 1），我们发现其N-末端和交叉环周围的泛素识别和蛋白水解的活性位点的大动态。N-末端进入和离开交叉环，表明其潜在的功能意义。我们的研究结果，包括那些从生化分析，表明，大的运动周围的活性位点有助于强烈的酶活性的效率。
Despite accumulating evidence that protein dynamics is indispensable for understanding the structural basis of biological activities, it remains challenging to visualize the spatial description of the dynamics and to associate transient conformations with their molecular functions. We have developed a new NMR protein structure determination method for the inference of multi-state conformations using multiple types of NMR data, including paramagnetic NMR and residual dipolar couplings, as well as conventional NOEs. Integration of these data in the structure calculation permits delineating accurate ensemble structures of biomacromolecules. Applying the method to the protein yeast ubiquitin hydrolase 1 (YUH1), we find large dynamics of its N-terminus and crossover loop surrounding the active site for ubiquitin-recognition and proteolysis. The N-terminus gets into and out of the crossover loop, suggesting their underlying functional significance. Our results, including those from biochemical analysis, show that large motion surrounding the active site contributes strongly to the efficiency of the enzymatic activity.