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© 2014 by The American Society for Biochemistry and Molecular Biology Inc. Cysteine peptidases are key proteolytic virulence factors of the periodontopathogen Porphyromonas gingivalis, which causes chronic periodontitis, the most prevalent dysbiosisdriven disease in humans. Two peptidases, gingipain K (Kgp) and R (RgpA and RgpB), which differ in their selectivity after lysines and arginines, respectively, collectively account for 85% of the extracellular proteolytic activity of P. gingivalis at the site of infection. Therefore, they are promising targets for the design of specific inhibitors. Although the structure of the catalytic domain of RgpB is known, little is known about Kgp, which shares only 27% sequence identity. We report the high resolution crystal structure of a competent fragment of Kgp encompassing the catalytic cysteine peptidase domain and a downstream immunoglobulin superfamily-like domain, which is required for folding and secretion of Kgp in vivo. The structure, which strikingly resembles a tooth, was serendipitously trapped with a fragment of a covalent inhibitor targeting the catalytic cysteine. This provided accurate insight into the active site and suggested that catalysis may require a catalytic triad, Cys477-His444-Asp388, rather than the cysteine-histidine dyad normally found in cysteine peptidases. In addition, a 20-Å-long solventfilled interior channel traverses the molecule and links the bottom of the specificity pocket with the molecular surface opposite the active site cleft. This channel, absent in RgpB, may enhance the plasticity of the enzyme, which would explain the much lower activity in vitro toward comparable specific synthetic substrates. Overall, the present results report the architecture and molecular determinants of the working mechanism of Kgp, including interaction with its substrates. ; This work was supported, in whole or in part, by National Institutes of Health Grant DE09761/DE/NIDCR. This work was also supported by Polish National Science Center Grant UMO-2012/04/A/NZ1/00051; Ministry of Science and Higher Education of Poland Grant 2137/7.PR-EU/2011/2; European Union Grants FP7-HEALTH-2010-261460 "Gums&Joints," FP7-PEOPLE-2011-ITN-290246 "RAPID," FP7-HEALTH-2012-306029-2 "TRIGGER," and POIG.02.01.00-12-064/08; Spanish Ministry of Economy and Competitiveness Grants BFU2012-32862 and BIO2013-49320-EXP; Spanish Ministry of Science and Education Grant CSD2006-00015; and National Government of Catalonia Grant 2014SGR9. Funding for data collection was provided in part by the European Synchrotron Radiation Facility (Grenoble, France) ; Peer Reviewed