title: Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC.
abstract: 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.
authors: Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; Swiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland;
authors: Hüseyin
authors: H
authors: Ilgü
authors: Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; Swiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland;
authors: Jean-Marc
authors: JM
authors: Jeckelmann
authors: Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.
authors: Vytautas
authors: V
authors: Gapsys
authors: Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; Swiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland;
authors: Zöhre
authors: Z
authors: Ucurum
authors: Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.
authors: Bert L
authors: BL
authors: de Groot
authors: Institute of Biochemistry and Molecular Medicine, University of Bern, CH-3012 Bern, Switzerland; Swiss National Centre of Competence in Research TransCure, University of Bern, CH-3012 Bern, Switzerland; dimitrios.fotiadis@ibmm.unibe.ch.
authors: Dimitrios
authors: D
authors: Fotiadis
mesh_terms: D000376:Agmatine / Q000737:chemistry; D026905:Amino Acid Transport Systems / Q000737:chemistry* / Q000235:genetics; D017920:Antiporters / Q000737:chemistry* / Q000235:genetics; D001120:Arginine / Q000737:chemistry / Q000235:genetics; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000737:chemistry / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics; D013379:Substrate Specificity
chemical_list: C476528:AdiC protein, E coli; D026905:Amino Acid Transport Systems; D017920:Antiporters; D029968:Escherichia coli Proteins; D000376:Agmatine; D001120:Arginine
keywords: X-ray structure; membrane protein; scintillation proximity assay; substrate binding; transporter