Porphyromonas gingivalis and Porphyromonas endodentalis are Gram-negative, black-pigmented anaerobic rods, which are the major pathogens of human chronic and periapical periodontitis, respectively, leading to loss of permanent teeth. P. gingivalis and P. endodentalis are asaccharolytic and do not ferment carbohydrates, thus requiring proteinaceous substrates as carbon and energy sources. These organisms combine the actions of several peptidases with different specificities to achieve proper nutritional requirements. An 81-kDa serine protease, called dipeptidyl peptidase 11 (DPP11), was recently discovered in P. gingivalis and P. endodentalis as an important enzyme for the energy metabolism of these bacteria1. It cleaves oligopeptides possessing aspartic acid or glutamic acid in the P1 position and displays preference for hydrophobic residues in the P2 position. In this study we aim at determining the X-ray crystal structures of these enzymes in the unbound form and in complex with different peptides, in order to elucidate the structural basis of their substrate specificity and affinity. We are also performing size exclusion chromatography followed by multiangle laser light scattering (SEC-MALLS), small angle X-ray scattering (SAXS) and circular dichroism experiments to assess the protein structure in solution. The overall fold of inactive mutants PgDPP11 S655A and PeDPP11 S652A are very similar and comprise two domains separated by a wide cleft: an upper entirely helical domain and a lower domain containing the catalytic triad. Both PgDPP11 S655A and PeDPP11 S652A behave as homodimers in solution and present a certain degree of flexibility between the subunits as well as between helical and catalytic domains. The binding data of different peptides to both enzymes are being investigated by means of microscale thermophoresis and isothermal titration calorimetry. Our data will help to elucidate the exact role of these enzymes in P. gingivalis and P. endodentalis energy metabolism and may provide a starting point for structure-based drug design.