title: Crystal Structure and Activity Studies of the C11 Cysteine Peptidase from Parabacteroides merdae in the Human Gut Microbiome.
abstract: Clan CD cysteine peptidases, a structurally related group of peptidases that include mammalian caspases, exhibit a wide range of important functions, along with a variety of specificities and activation mechanisms. However, for the clostripain family (denoted C11), little is currently known. Here, we describe the first crystal structure of a C11 protein from the human gut bacterium, Parabacteroides merdae (PmC11), determined to 1.7-Å resolution. PmC11 is a monomeric cysteine peptidase that comprises an extended caspase-like α/β/α sandwich and an unusual C-terminal domain. It shares core structural elements with clan CD cysteine peptidases but otherwise structurally differs from the other families in the clan. These studies also revealed a well ordered break in the polypeptide chain at Lys(147), resulting in a large conformational rearrangement close to the active site. Biochemical and kinetic analysis revealed Lys(147) to be an intramolecular processing site at which cleavage is required for full activation of the enzyme, suggesting an autoinhibitory mechanism for self-preservation. PmC11 has an acidic binding pocket and a preference for basic substrates, and accepts substrates with Arg and Lys in P1 and does not require Ca(2+) for activity. Collectively, these data provide insights into the mechanism and activity of PmC11 and a detailed framework for studies on C11 peptidases from other phylogenetic kingdoms.
authors.affiliation: From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom.
authors.forename: Karen
authors.identifier: http://orcid.org/0000-0002-9841-4943
authors.initials: K
authors.lastname: McLuskey
authors.affiliation: From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom.
authors.forename: Jaspreet S
authors.identifier: http://orcid.org/0000-0002-2219-7655
authors.initials: JS
authors.lastname: Grewal
authors.affiliation: the Joint Center for Structural Genomics, the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.
authors.forename: Debanu
authors.initials: D
authors.lastname: Das
authors.affiliation: the Joint Center for Structural Genomics, the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, the Program on Bioinformatics and Systems Biology, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California 92037.
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
authors.affiliation: the Joint Center for Structural Genomics, the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, the Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California 92121, and.
authors.forename: Scott A
authors.initials: SA
authors.lastname: Lesley
authors.affiliation: the Joint Center for Structural Genomics, the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.
authors.forename: Ashley M
authors.initials: AM
authors.lastname: Deacon
authors.affiliation: the Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, United Kingdom.
authors.forename: Graham H
authors.initials: GH
authors.lastname: Coombs
authors.affiliation: the Joint Center for Structural Genomics, the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Elsliger
authors.affiliation: the Joint Center for Structural Genomics, the Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California 92037, wilson@scripps.edu.
authors.forename: Ian A
authors.initials: IA
authors.lastname: Wilson
authors.affiliation: From the Wellcome Trust Centre for Molecular Parasitology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, United Kingdom, the Department of Biology, Centre for Immunology and Infection, University of York, Wentworth Way, Heslington, York YO10 5DD, United Kingdom, jeremy.mottram@york.ac.uk.
authors.forename: Jeremy C
authors.identifier: http://orcid.org/0000-0001-5574-3766
authors.initials: JC
authors.lastname: Mottram
mesh_terms: D001426:Bacterial Proteins / Q000737:chemistry*; D001438:Bacteroidaceae / Q000201:enzymology*; D018360:Crystallography, X-Ray; D057056:Cysteine Proteases / Q000737:chemistry*; D000069196:Gastrointestinal Microbiome; D006801:Humans; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary
chemical_list: D001426:Bacterial Proteins; D057056:Cysteine Proteases
keywords: C-terminal domain (carboxyl tail domain, CTD); active site; crystal structure; cysteine protease; domain; enzyme; kinteoplast; proteolysis