文章基本信息

标题：Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination
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作者：Michael J. Sheedlo ; Jiazhang Qiu ; Yunhao Tan 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2015
卷号：112
期号：49
页码：15090-15095
DOI：10.1073/pnas.1514568112
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：SignificanceUbiquitination and deubiquitination have emerged in recent years as novel targets for the design of therapeutic agents. To our knowledge, the structure of the deubiquitinase (DUB) domain of SdeA represents the first prokaryotic DUB determined and will thus potentially serve as a model for other bacterial deubiquitinating enzymes for use in structure-guided drug design. Legionella pneumophila ubiquitin E3 ligases play important roles in the biogenesis of the phagosome permissive for bacterial replication. The discovery of effectors with DUB activity highlights the importance of modulation of host processes in a regulated and balanced manner. Manipulation of the hosts ubiquitin network is emerging as an important strategy for counteracting and repurposing the posttranslational modification machineries of the host by pathogens. Ubiquitin E3 ligases encoded by infectious agents are well known, as are a variety of viral deubiquitinases (DUBs). Bacterial DUBs have been discovered, but little is known about the structure and mechanism underlying their ubiquitin recognition. In this report, we found that members of the Legionella pneumophila SidE effector family harbor a DUB module important for ubiquitin dynamics on the bacterial phagosome. Structural analysis of this domain alone and in complex with ubiquitin vinyl methyl ester (Ub-VME) reveals unique molecular contacts used in ubiquitin recognition. Instead of relying on the Ile44 patch of ubiquitin, as commonly used in eukaryotic counterparts, the SdeADub module engages Gln40 of ubiquitin. The architecture of the active-site cleft presents an open arrangement with conformational plasticity, permitting deubiquitination of three of the most abundant polyubiquitin chains, with a distinct preference for Lys63 linkages. We have shown that this preference enables efficient removal of Lys63 linkages from the phagosomal surface. Remarkably, the structure reveals by far the most parsimonious use of molecular contacts to achieve deubiquitination, with less than 1,000 [IMG]f1.gif" ALT="A" BORDER="0">2 of accessible surface area buried upon complex formation with ubiquitin. This type of molecular recognition appears to enable dual specificity toward ubiquitin and the ubiquitin-like modifier NEDD8.
关键词：type IV secretion ; ubiquitination ; Legionella ; phagosome ; deubiquitinase