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

Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Gapsys, Vytautas; Ucurum Fotiadis, Zöhre; de Groot, Bert L; Fotiadis, Dimitrios José (2016). Insights into the molecular basis for substrate binding and specificity of the wild-type L-arginine/agmatine antiporter AdiC. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 113(37), pp. 10358-10363. National Academy of Sciences NAS 10.1073/pnas.1605442113

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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.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Faculty Institutions > NCCR TransCure
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Biochemistry and Molecular Medicine

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Ilgü, Hüseyin; Jeckelmann, Jean-Marc; Ucurum Fotiadis, Zöhre and Fotiadis, Dimitrios José


500 Science > 570 Life sciences; biology
600 Technology > 610 Medicine & health




National Academy of Sciences NAS




Barbara Järmann-Bangerter

Date Deposited:

19 Apr 2017 09:43

Last Modified:

19 Apr 2017 09:43

Publisher DOI:


PubMed ID:


Uncontrolled Keywords:

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




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