Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 49; pp. 15090 - 15095
• Main Authors: Sheedlo, Michael J., Qiu, Jiazhang, Tan, Yunhao, Paul, Lake N., Luo, Zhao-Qing, Das, Chittaranjan
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 08.12.2015; National Acad Sciences
• Subjects: Amino Acid Sequence; Bacteria; BASIC BIOLOGICAL SCIENCES; Biological Sciences; deubiquitinase; Eukaryotes; HEK293 Cells; Humans; Legionella; Legionella pneumophila; Legionella pneumophila - enzymology; Membrane Proteins - metabolism; Molecular Sequence Data; Molecules; phagosome; Phagosomes - metabolism; type IV secretion; Ubiquitin - chemistry; Ubiquitin-Specific Proteases - metabolism; Ubiquitination; phagosome; Legionella; type IV secretion; ubiquitination; deubiquitinase
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1514568112

Manipulation of the host’s 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 theLegionella pneumophilaSidE 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 SdeADubmodule 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 Ų 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.