Structural basis for the drug extrusion mechanism by a MATE multidrug transporter

Several X-ray crystal structures of an H + -driven multidrug and toxic compound extrusion (MATE) transporter from Pyrococcus furiosus are presented, whose complex structure with macrocyclic peptides may help facilitate the discovery of efficient inhibitors of MATE transporters. MATE drug transporter structures Transporters of the MATE (multidrug and toxic compound extrusion) family confer multidrug resistance to bacterial pathogens and cancer cells. Osamu Nureki and colleagues have now solved X-ray crystal structures of a H + -driven MATE transporter from the hyperthermophilic archaean Pyrococcus furiosus in two distinct apo-form conformations: the transporter in the presence of a derivative of the antibacterial drug norfloxacin, and the transporter in the presence of three newly discovered inhibitory macrocyclic peptides. This collection of structures may help to facilitate the discovery of MATE transporter antagonists that could counter resistance to antibacterial and anticancer drugs. Multidrug and toxic compound extrusion (MATE) family transporters are conserved in the three primary domains of life (Archaea, Bacteria and Eukarya), and export xenobiotics using an electrochemical gradient of H + or Na + across the membrane 1 , 2 . MATE transporters confer multidrug resistance to bacterial pathogens 3 , 4 , 5 , 6 and cancer cells 7 , thus causing critical reductions in the therapeutic efficacies of antibiotics and anti-cancer drugs, respectively. Therefore, the development of MATE inhibitors has long been awaited in the field of clinical medicine 8 , 9 . Here we present the crystal structures of the H + -driven MATE transporter from Pyrococcus furiosus in two distinct apo-form conformations, and in complexes with a derivative of the antibacterial drug norfloxacin and three in vitro selected thioether-macrocyclic peptides, at 2.1–3.0 Å resolutions. The structures, combined with functional analyses, show that the protonation of Asp 41 on the amino (N)-terminal lobe induces the bending of TM1, which in turn collapses the N-lobe cavity, thereby extruding the substrate drug to the extracellular space. Moreover, the macrocyclic peptides bind the central cleft in distinct manners, which correlate with their inhibitory activities. The strongest inhibitory peptide that occupies the N-lobe cavity may pave the way towards the development of efficient inhibitors against MATE transporters.