Structure of the AcrAB–TolC multidrug efflux pump

Many bacteria are able to survive in the presence of antibiotics in part because they possess pumps that can remove a broad range of small molecules; here, the structure of one such pump, AcrAB–TolC, is determined using X-ray crystallography and cryo-electron microscopy. Many bacteria are able to survive in the presence of antibiotics and other toxic compounds because they possess versatile energy-dependent transmembrane pumps. For example, the AcrAB–TolC efflux pump, which spans the inner and outer membranes of the bacterium, is able to transport a broad range of structurally unrelated small molecules/drugs out of some Gram-negative bacteria. The pump is comprised of an outer-membrane channel (TolC), a secondary transporter (AcrB; located in the inner membrane), and AcrA, a periplasmic protein that acts as a bridge for these two integral membrane proteins. In this paper, the authors solve an X-ray crystal structure of AcrB bound to AcrZ (a small protein that appears to alter the substrate preferences of AcrB) and a cryo-EM structure of the entire 771 kDa efflux pump. The capacity of numerous bacterial species to tolerate antibiotics and other toxic compounds arises in part from the activity of energy-dependent transporters. In Gram-negative bacteria, many of these transporters form multicomponent ‘pumps’ that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component1,2,3,4,5,6,7. A model system for such a pump is the acridine resistance complex of Escherichia coli1. This pump assembly comprises the outer-membrane channel TolC, the secondary transporter AcrB located in the inner membrane, and the periplasmic AcrA, which bridges these two integral membrane proteins. The AcrAB–TolC efflux pump is able to transport vectorially a diverse array of compounds with little chemical similarity, thus conferring resistance to a broad spectrum of antibiotics. Homologous complexes are found in many Gram-negative species, including in animal and plant pathogens. Crystal structures are available for the individual components of the pump2,3,4,5,6,7 and have provided insights into substrate recognition, energy coupling and the transduction of conformational changes associated with the transport process. However, how the subunits are organized in the pump, their stoichiometry and the details of their interactions are not known. Here we present the pseudo-atomic structure of a complete multidrug efflux pump in complex with a modulatory protein partner8 from E. coli. The model defines the quaternary organization of the pump, identifies key domain interactions, and suggests a cooperative process for channel assembly and opening. These findings illuminate the basis for drug resistance in numerous pathogenic bacterial species.