title: Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site.
abstract: OmpT from Escherichia coli belongs to a family of highly homologous outer membrane proteases, known as omptins, which are implicated in the virulence of several pathogenic Gram-negative bacteria. Here we present the crystal structure of OmpT, which shows a 10-stranded antiparallel beta-barrel that protrudes far from the lipid bilayer into the extracellular space. We identified a putative binding site for lipopolysaccharide, a molecule that is essential for OmpT activity. The proteolytic site is located in a groove at the extracellular top of the vase-shaped beta-barrel. Based on the constellation of active site residues, we propose a novel proteolytic mechanism, involving a His-Asp dyad and an Asp-Asp couple that activate a putative nucleophilic water molecule. The active site is fully conserved within the omptin family. Therefore, the structure described here provides a sound basis for the design of drugs against omptin-mediated bacterial pathogenesis. Coordinates are in the Protein Data Bank (accession No. 1I78)
authors.affiliation: Department of Crystal and Structural Chemistry, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
authors.forename: L
authors.initials: L
authors.lastname: Vandeputte-Rutten
authors.forename: R A
authors.initials: RA
authors.lastname: Kramer
authors.forename: J
authors.initials: J
authors.lastname: Kroon
authors.forename: N
authors.initials: N
authors.lastname: Dekker
authors.forename: M R
authors.initials: MR
authors.lastname: Egmond
authors.forename: P
authors.initials: P
authors.lastname: Gros
mesh_terms: D000595:Amino Acid Sequence; D001224:Aspartic Acid / Q000737:chemistry; D001665:Binding Sites; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D006639:Histidine / Q000737:chemistry; D008070:Lipopolysaccharides / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D012697:Serine Endopeptidases / Q000737:chemistry* / Q000378:metabolism
chemical_list: D008070:Lipopolysaccharides; D001224:Aspartic Acid; D006639:Histidine; D012697:Serine Endopeptidases; C057840:omptin outer membrane protease