Biochemical and Structural Analysis of the Bacterial Enzyme Succinyl-Diaminopimelate Desuccinylase (DapE) from

There is an urgent need for new antibiotics given the rise of antibiotic resistance, and succinyl-diaminopimelate desuccinylase (DapE, E.C. 3.5.1.18) has emerged as a promising bacterial enzyme target. DapE from (DapE) has been studied and inhibitors identified, but it is essential to explore DapE from different species to assess selective versus broad-spectrum therapeutics. We have determined the structure of DapE from the ESKAPE pathogen (DapE) and studied inhibition by known inhibitors of DapE. DapE is inhibited by captopril and sulfate comparable to DapE, but DapE was not significantly inhibited by a known indoline sulfonamide DapE inhibitor. Captopril and sulfate both stabilize DapE by increasing the thermal melting temperature () in thermal shift assays. By contrast, sulfate decreases the stability of the DapE enzyme, whereas captopril increases the stability. Further, we report two crystal structures of selenomethionine-substituted DapE in the closed conformation, one with DapE in complex with succinate derived from enzymatic hydrolysis of -methyl-l,l-SDAP substrate and acetate (PDB code 7T1Q, 2.25 Å resolution), and a crystal structure of DapE with bound succinate along with l-(S)-lactate, a product of degradation of citric acid from the crystallization buffer during X-ray irradiation (PDB code 8F8O, 2.10 Å resolution).