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Mechanism of substrate recognition and transport by an amino acid antiporter

Abstract

In extremely acidic environments, enteric bacteria such as Escherichia coli rely on the amino acid antiporter AdiC to expel protons by exchanging intracellular agmatine (Agm2+) for extracellular arginine (Arg+)1,2,3. AdiC is a representative member of the amino acid-polyamine-organocation (APC) superfamily of membrane transporters4,5. The structure of substrate-free AdiC revealed a homodimeric assembly, with each protomer containing 12 transmembrane segments and existing in an outward-open conformation6,7. The overall folding of AdiC is similar to that of the Na+-coupled symporters8,9,10,11. Despite these advances, it remains unclear how the substrate (arginine or agmatine) is recognized and transported by AdiC. Here we report the crystal structure of an E. coli AdiC variant bound to Arg at 3.0 Å resolution. The positively charged Arg is enclosed in an acidic binding chamber, with the head groups of Arg hydrogen-bonded to main chain atoms of AdiC and the aliphatic portion of Arg stacked by hydrophobic side chains of highly conserved residues. Arg binding induces pronounced structural rearrangement in transmembrane helix 6 (TM6) and, to a lesser extent, TM2 and TM10, resulting in an occluded conformation. Structural analysis identified three potential gates, involving four aromatic residues and Glu 208, which may work in concert to differentially regulate the upload and release of Arg and Agm.

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Figure 1: Structure of AdiC bound to Arg.
Figure 2: Recognition of Arg by conserved amino acids.
Figure 3: Conformational changes of AdiC upon binding of Arg.
Figure 4: A proposed model for Arg-Agm exchange.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

The atomic coordinates of AdiC bound to Arg have been deposited in the Protein Data Bank under the accession code 3L1L.

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Acknowledgements

We thank C. Miller and Y. Xiong for discussion and exchange of information, N. Shimizu, T. Kumasaka and S. Baba at the Spring-8 beamline BL41XU for on-site assistance, and N. Yan for discussion and comments on the manuscript. This work was supported by the Ministry of Science and Technology (grant no. 2009CB918801), Tsinghua University 985 Phase II funds, National Natural Science Foundation, and Beijing Municipal Commissions of Education and Science and Technology.

Author Contributions Experiments were performed by X.G., L.Z., X.J., F.L., C.Y., X.Z. and J.W. Data were analysed by X.G., L.Z., X.J., J.W. and Y.S. The manuscript was prepared by X.G., L.Z. and Y.S.

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Correspondence to Yigong Shi.

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This file contains Supplementary Tables 1-3, Supplementary Figures 1-12 with Legends and Supplementary References. (PDF 2651 kb)

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Gao, X., Zhou, L., Jiao, X. et al. Mechanism of substrate recognition and transport by an amino acid antiporter. Nature 463, 828–832 (2010). https://doi.org/10.1038/nature08741

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