An embedded lipid in the multidrug transporter LmrP suggests a mechanism for polyspecificity

Nat Struct Mol Biol. 2020 Sep;27(9):829-835. doi: 10.1038/s41594-020-0464-y. Epub 2020 Jul 27.

Abstract

Multidrug efflux pumps present a challenge to the treatment of bacterial infections, making it vitally important to understand their mechanism of action. Here, we investigate the nature of substrate binding within Lactococcus lactis LmrP, a prototypical multidrug transporter of the major facilitator superfamily. We determined the crystal structure of LmrP in a ligand-bound outward-open state and observed an embedded lipid in the binding cavity of LmrP, an observation supported by native mass spectrometry analyses. Molecular dynamics simulations suggest that the anionic lipid stabilizes the observed ligand-bound structure. Mutants engineered to disrupt binding of the embedded lipid display reduced transport of some, but not all, antibiotic substrates. Our results suggest that a lipid within the binding cavity could provide a malleable hydrophobic component that allows adaptation to the presence of different substrates, helping to explain the broad specificity of this protein and possibly other multidrug transporters.

Publication types

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

MeSH terms

  • Anti-Bacterial Agents / metabolism*
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / metabolism*
  • Binding Sites
  • Biological Transport
  • Crystallography, X-Ray
  • Lactococcus lactis / chemistry
  • Lactococcus lactis / metabolism*
  • Ligands
  • Membrane Transport Proteins / chemistry
  • Membrane Transport Proteins / metabolism*
  • Molecular Dynamics Simulation
  • Phosphatidylglycerols / chemistry
  • Phosphatidylglycerols / metabolism*
  • Protein Conformation
  • Substrate Specificity

Substances

  • Anti-Bacterial Agents
  • Bacterial Proteins
  • Ligands
  • Membrane Transport Proteins
  • Phosphatidylglycerols