Boomsma Wouter, Nielsen Sofie V, Lindorff-Larsen Kresten, Hartmann-Petersen Rasmus, Ellgaard Lars
Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen , Copenhagen , Denmark.
PeerJ. 2016 Feb 25;4:e1725. doi: 10.7717/peerj.1725. eCollection 2016.
The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work indicates that San1 is not a unique case, and that several other yeast and human E3 ligases have sequence properties that may allow them to recognize substrates by a similar mechanism as San1.
泛素 - 蛋白酶体系统将错误折叠的蛋白质作为降解目标。由于此类蛋白质的积累可能对细胞有害，因此迅速清除它们很重要。E3泛素 - 蛋白连接酶通过将底物与E2泛素结合酶聚集在一起介导底物泛素化，E2泛素结合酶将泛素转移到底物上。对于错误折叠的蛋白质，底物识别通常委托给分子伴侣，分子伴侣随后与特定的E3连接酶相互作用。一个重要的例外是酵母E3连接酶San1。San1具有广泛的内在无序区域，这些区域既提供构象灵活性，又提供直接识别大量不同构象的错误折叠靶标的位点。到目前为止，尚不知道San1的哺乳动物直系同源物，也不清楚其他E3连接酶是否利用无序区域进行底物识别。在这里，我们进行了一项生物信息学分析，以检查600多种人类和酿酒酵母E3连接酶，以识别在功能和/或底物识别机制方面与San1相似的酶。发现最初基于序列的数据库搜索主要基于其有序区域的同源性来检测候选物，并且没有捕捉到编码San1功能机制的独特无序模式。然而，通过专门搜索San1序列的关键特征，例如嵌入预计适合底物相互作用的短片段的长内在无序区域，我们鉴定了几种具有这些特征的E3连接酶。我们的初步分析表明，San1的另一个显著特征与几种候选E3连接酶相同：长片段的完全赖氨酸抑制，这在San1中限制了自身泛素化。我们将这些特征编码为San1相似性评分，并提出了一组蛋白质，它们可能是人类中San1对应物的合理候选者。总之，我们的工作表明San1并非独一无二，其他几种酵母和人类E3连接酶具有的序列特性可能使它们能够通过与San1类似的机制识别底物。
