Crystal structure of the outer membrane protease OmpT from Escherichia coli suggests a novel catalytic site

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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 β‐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 β‐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)