Cryo‐EM structure of antibacterial efflux transporter QacA from Staphylococcus aureus reveals a novel extracellular loop with allosteric role

Abstract

Bacterial pathogenicity relies on the export of antibacterial compounds by broad‐specificity transporters; however, the molecular determinants of this resistance remain unclear. Here, structural work describes unique features of the proton‐coupled‐efflux transporter QacA in Staphylococcus aureus that reveal a conserved allosteric gating mechanism, and suggest new therapeutic approaches to combat systemic infection. Cryo‐EM structure of QacA stabilized in outward‐open state was elucidated in complex with two single‐domain camelid antibodies that served as fiducial markers. QacA displays a unique extracellular α‐helical hairpin loop (EL7) between transmembrane helices 13 and 14 that is observed in a subset of drug:proton antiporters. Removal of EL7 leads to loss of efflux activity that can be regained by translocating EL7 regions from related transporters. Comparison of the outward‐open QacA structure with the inward‐open model reveals the formation of the EL7‐EL1 interface that serves to close the extracellular gate during the efflux cycle.