Sequence and Structural Determinants of Ligand-dependent Alternating Access of a MATE Transporter

MATE transporters are ubiquitous ion-coupled antiporters that extrude structurally- and chemically-dissimilar molecules and have been implicated in conferring multidrug resistance. Here, we integrate Double Electron Electron Resonance (DEER) in conjunction with functional assays and site-directed mutagenesis of conserved residues to illuminate principles of ligand-dependent alternating access of PfMATE, a proton-coupled MATE from the hyperthermophilic archaeon Pyrococcus furiosus. Pairs of spin labels monitoring the two sides of the transporter reconstituted into nanodiscs reveal large amplitude movement of helices that alter the orientation of a putative substrate binding cavity. We found that acidic pH favors formation of an inward-facing (IF) conformation, whereas elevated pH (>7) and the substrate rhodamine 6G stabilizes an outward-facing (OF) conformation. PfMATE isomerization between outward-facing and inward-facing conformations is driven by protonation of a previously unidentified intracellular glutamate residue that is critical for drug resistance. Our results can be framed in a mechanistic model of transport that addresses central aspects of ligand coupling and alternating access.