Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
Nat Commun. 2018 Jul 12;9(1):2696. doi: 10.1038/s41467-018-05198-1.
While protein ubiquitination was long believed to be a truly eukaryotic feature, recently sequenced genomes revealed complete ubiquitin (Ub) modification operons in archaea. Here, we present the structural and mechanistic characterization of an archaeal Rpn11 deubiquitinase from Caldiarchaeum subterraneum, CsRpn11, and its role in the processing of CsUb precursor and ubiquitinated proteins. CsRpn11 activity is affected by the catalytic metal ion type, small molecule inhibitors, sequence characteristics at the cleavage site, and the folding state of CsUb-conjugated proteins. Comparison of CsRpn11 and CsRpn11-CsUb crystal structures reveals a crucial conformational switch in the CsRpn11 Ins-1 site, which positions CsUb for catalysis. The presence of this transition in a primordial soluble Rpn11 thus predates the evolution of eukaryotic Rpn11 immobilized in the proteasomal lid. Complementing phylogenetic studies, which designate CsRpn11 and CsUb as close homologs of the respective eukaryotic proteins, our results provide experimental support for an archaeal origin of protein ubiquitination.
虽然蛋白质泛素化长期以来被认为是真正的真核生物特征，但最近测序的基因组揭示了古菌中完整的泛素（Ub）修饰操纵子。在这里，我们介绍了来自 Caldiarchaeum subterraneum 的古菌 Rpn11 去泛素化酶 CsRpn11 的结构和机制特征，以及其在 CsUb 前体和泛素化蛋白加工中的作用。CsRpn11 的活性受到催化金属离子类型、小分子抑制剂、切割位点的序列特征以及 CsUb 缀合蛋白折叠状态的影响。CsRpn11 和 CsRpn11-CsUb 晶体结构的比较揭示了 CsRpn11Ins-1 位点的关键构象转换，该转换将 CsUb 定位用于催化。这种原始可溶性 Rpn11 中的这种转变先于真核生物 Rpn11 固定在蛋白酶体盖中的进化。补充系统发育研究，将 CsRpn11 和 CsUb 分别指定为各自真核蛋白的密切同源物，我们的结果为蛋白质泛素化的古菌起源提供了实验支持。
