Structures of a Na+-coupled, substrate-bound MATE multidrug transporter

Proc Natl Acad Sci U S A. 2013 Feb 5;110(6):2099-104. doi: 10.1073/pnas.1219901110. Epub 2013 Jan 22.


Multidrug transporters belonging to the multidrug and toxic compound extrusion (MATE) family expel dissimilar lipophilic and cationic drugs across cell membranes by dissipating a preexisting Na(+) or H(+) gradient. Despite its clinical relevance, the transport mechanism of MATE proteins remains poorly understood, largely owing to a lack of structural information on the substrate-bound transporter. Here we report crystal structures of a Na(+)-coupled MATE transporter NorM from Neisseria gonorrheae in complexes with three distinct translocation substrates (ethidium, rhodamine 6G, and tetraphenylphosphonium), as well as Cs(+) (a Na(+) congener), all captured in extracellular-facing and drug-bound states. The structures revealed a multidrug-binding cavity festooned with four negatively charged amino acids and surprisingly limited hydrophobic moieties, in stark contrast to the general belief that aromatic amino acids play a prominent role in multidrug recognition. Furthermore, we discovered an uncommon cation-π interaction in the Na(+)-binding site located outside the drug-binding cavity and validated the biological relevance of both the substrate- and cation-binding sites by conducting drug resistance and transport assays. Additionally, we uncovered potential rearrangement of at least two transmembrane helices upon Na(+)-induced drug export. Based on our structural and functional analyses, we suggest that Na(+) triggers multidrug extrusion by inducing protein conformational changes rather than by directly competing for the substrate-binding amino acids. This scenario is distinct from the canonical antiport mechanism, in which both substrate and counterion compete for a shared binding site in the transporter. Collectively, our findings provide an important step toward a detailed and mechanistic understanding of multidrug transport.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution
  • Antiporters / chemistry*
  • Antiporters / genetics
  • Antiporters / metabolism*
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Cesium / metabolism
  • Crystallography, X-Ray
  • Drug Resistance, Multiple, Bacterial / genetics
  • Models, Molecular
  • Molecular Sequence Data
  • Mutagenesis, Site-Directed
  • Neisseria gonorrhoeae / drug effects
  • Neisseria gonorrhoeae / genetics
  • Neisseria gonorrhoeae / metabolism
  • Protein Conformation
  • Sequence Homology, Amino Acid
  • Sodium / metabolism
  • Static Electricity


  • Antiporters
  • Bacterial Proteins
  • NorM protein, bacteria
  • Cesium
  • Sodium

Associated data

  • PDB/4HUK
  • PDB/4HUL
  • PDB/4HUM
  • PDB/4HUN