Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC

Proc Natl Acad Sci U S A. 2016 Sep 13;113(37):10358-63. doi: 10.1073/pnas.1605442113. Epub 2016 Aug 31.


Pathogenic enterobacteria need to survive the extreme acidity of the stomach to successfully colonize the human gut. Enteric bacteria circumvent the gastric acid barrier by activating extreme acid-resistance responses, such as the arginine-dependent acid resistance system. In this response, l-arginine is decarboxylated to agmatine, thereby consuming one proton from the cytoplasm. In Escherichia coli, the l-arginine/agmatine antiporter AdiC facilitates the export of agmatine in exchange of l-arginine, thus providing substrates for further removal of protons from the cytoplasm and balancing the intracellular pH. We have solved the crystal structures of wild-type AdiC in the presence and absence of the substrate agmatine at 2.6-Å and 2.2-Å resolution, respectively. The high-resolution structures made possible the identification of crucial water molecules in the substrate-binding sites, unveiling their functional roles for agmatine release and structure stabilization, which was further corroborated by molecular dynamics simulations. Structural analysis combined with site-directed mutagenesis and the scintillation proximity radioligand binding assay improved our understanding of substrate binding and specificity of the wild-type l-arginine/agmatine antiporter AdiC. Finally, we present a potential mechanism for conformational changes of the AdiC transport cycle involved in the release of agmatine into the periplasmic space of E. coli.

Keywords: X-ray structure; membrane protein; scintillation proximity assay; substrate binding; transporter.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Agmatine / chemistry
  • Amino Acid Transport Systems / chemistry*
  • Amino Acid Transport Systems / genetics
  • Antiporters / chemistry*
  • Antiporters / genetics
  • Arginine / chemistry
  • Arginine / genetics
  • Binding Sites
  • Crystallography, X-Ray
  • Escherichia coli / chemistry
  • Escherichia coli / genetics
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / genetics
  • Substrate Specificity


  • AdiC protein, E coli
  • Amino Acid Transport Systems
  • Antiporters
  • Escherichia coli Proteins
  • Agmatine
  • Arginine

Associated data

  • PDB/5J4I
  • PDB/5J4N