The alternating-access mechanism of MFS transporters arises from inverted-topology repeats

J Mol Biol. 2011 Apr 15;407(5):698-715. doi: 10.1016/j.jmb.2011.02.008. Epub 2011 Feb 18.


Lactose permease (LacY) is the prototype of the major facilitator superfamily (MFS) of secondary transporters. Available structures of LacY reveal a state in which the substrate is exposed to the cytoplasm but is occluded from the periplasm. However, the alternating-access transport mechanism requires the existence of a periplasm-facing state. We recently showed that inverted-topology structural repeats provide the foundation for the mechanisms of two transporter families with folds distinct from the MFS. Here, we generated a structural model of LacY by swapping the conformations of inverted-topology repeats identified in its two domains. The model exhibits all required properties of an outward-facing conformation, i.e., closure of the binding site to the cytoplasm and exposure to the periplasm. Furthermore, the model agrees with double electron-electron resonance distance changes, accessibility to cysteine-modifying reagents, cysteine cross-linking data, and a recent structure of a distantly related transporter. Analysis of the intradomain differences between the two states suggests a role for conserved sequence motifs in occluding the central pathway through kinking of the pore-lining helices. In addition, predicted re-pairing of critical salt-bridging residues in the binding sites agrees remarkably well with previous proposals, allowing a description of the proton/sugar transport mechanism. More fundamentally, our model demonstrates that inverted-topology repeats provide the foundation for the alternating-access mechanisms of MFS transporters.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crystallography, X-Ray
  • Escherichia coli / enzymology*
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Escherichia coli Proteins / metabolism
  • Ethylmaleimide / chemistry
  • Models, Molecular
  • Monosaccharide Transport Proteins / chemistry*
  • Monosaccharide Transport Proteins / genetics
  • Monosaccharide Transport Proteins / metabolism
  • Protein Structure, Secondary*
  • Protein Structure, Tertiary*
  • Solvents / chemistry
  • Symporters / chemistry*
  • Symporters / genetics
  • Symporters / metabolism


  • Escherichia coli Proteins
  • FucP protein, E coli
  • LacY protein, E coli
  • Monosaccharide Transport Proteins
  • Solvents
  • Symporters
  • Ethylmaleimide