title: Structural basis of substrate recognition by a bacterial deubiquitinase important for dynamics of phagosome ubiquitination.
abstract: 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 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 Å(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.
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907;
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Sheedlo
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;
authors.forename: Jiazhang
authors.initials: J
authors.lastname: Qiu
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907;
authors.forename: Yunhao
authors.initials: Y
authors.lastname: Tan
authors.affiliation: Bindley Biosciences Center, Purdue University, West Lafayette, IN 47907.
authors.forename: Lake N
authors.initials: LN
authors.lastname: Paul
authors.affiliation: Department of Biological Sciences, Purdue University, West Lafayette, IN 47907; luoz@purdue.edu cdas@purdue.edu.
authors.forename: Zhao-Qing
authors.initials: ZQ
authors.lastname: Luo
authors.affiliation: Department of Chemistry, Purdue University, West Lafayette, IN 47907; luoz@purdue.edu cdas@purdue.edu.
authors.forename: Chittaranjan
authors.initials: C
authors.lastname: Das
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins; D057809:HEK293 Cells; D006801:Humans; D016952:Legionella pneumophila / Q000201:enzymology*; D008565:Membrane Proteins / Q000378:metabolism*; D008969:Molecular Sequence Data; D010588:Phagosomes / Q000378:metabolism*; D025801:Ubiquitin / Q000737:chemistry; D064570:Ubiquitin-Specific Proteases / Q000378:metabolism*; D054875:Ubiquitination
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins; C503174:SdeA protein, Legionella pneumophila; D025801:Ubiquitin; D064570:Ubiquitin-Specific Proteases
keywords: Legionella; deubiquitinase; phagosome; type IV secretion; ubiquitination