Structure and dynamics of Burkholderia pseudomallei OXA-57, a distinctive low efficiency class D β-lactamase with carbapenem-hydrolyzing activity

The Gram-negative bacterium Burkholderia pseudomallei causes the severe disease melioidosis. β-Lactams, including carbapenems, are the primary treatment, but are susceptible to chromosomal β-lactamases, including the class D enzyme OXA-57. Here we show recombinant OXA-57 is active towards penicillins and first-generation cephalosporins, slowly hydrolyzes carbapenems including imipenem and meropenem, but is inactive towards oxyimino-cephalosporins (e.g., ceftazidime). Unlike many OXA enzymes, OXA-57 is sensitive to the mechanism-based inhibitor clavulanic acid, but less so to the diazabicyclooctane avibactam and not to the cyclic boronate vaborbactam. Crystal structures of covalent OXA-57:avibactam and OXA-57:meropenem complexes reveal limited hydrogen- bonding interactions with bound ligands. In molecular dynamics simulations, bound meropenem is mobile, while the water necessary for deacylation has only limited active site access. These observations are consistent with the low level of meropenem turnover, supporting proposals that OXA β-lactamases generally possess limited carbapenemase activity, and highlight the potential importance of OXA-57 in B. pseudomallei β-lactam resistance.