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

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

Author information

1
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;
2
Computational Biomolecular Dynamics Group, Max-Planck-Institute for Biophysical Chemistry, D-37077 Goettingen, Germany.
3
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.

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.

KEYWORDS:

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

PMID:
27582465
PMCID:
PMC5027449
DOI:
10.1073/pnas.1605442113
[Indexed for MEDLINE]
Free PMC Article

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