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Structure of a prokaryotic virtual proton pump at 3.2 Å resolution

Abstract

To reach the mammalian gut, enteric bacteria must pass through the stomach. Many such organisms survive exposure to the harsh gastric environment (pH 1.5–4) by mounting extreme acid-resistance responses, one of which, the arginine-dependent system of Escherichia coli, has been studied at levels of cellular physiology, molecular genetics and protein biochemistry1,2,3,4,5,6,7. This multiprotein system keeps the cytoplasm above pH 5 during acid challenge by continually pumping protons out of the cell using the free energy of arginine decarboxylation. At the heart of the process is a ‘virtual proton pump’8 in the inner membrane, called AdiC3,4, that imports l-arginine from the gastric juice and exports its decarboxylation product agmatine. AdiC belongs to the APC superfamily of membrane proteins6,7,9, which transports amino acids, polyamines and organic cations in a multitude of biological roles, including delivery of arginine for nitric oxide synthesis10, facilitation of insulin release from pancreatic β-cells11, and, when inappropriately overexpressed, provisioning of certain fast-growing neoplastic cells with amino acids12,13. High-resolution structures and detailed transport mechanisms of APC transporters are currently unknown. Here we describe a crystal structure of AdiC at 3.2 Å resolution. The protein is captured in an outward-open, substrate-free conformation with transmembrane architecture remarkably similar to that seen in four other families of apparently unrelated transport proteins.

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Figure 1: AdiC physiology and function.
Figure 2: Structure of AdiC.
Figure 3: Structural alignment of AdiC with four transporter families.
Figure 4: AdiC cavity in outward-open conformation.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors of the AdiC–Fab complex have been deposited in the Protein Data Bank under accession number 3HQK.

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Acknowledgements

Y.F. was supported by NIH grant T32 NS 07292. We appreciate the support of the beamline scientists at the Advanced Photon Source (GM-CAT, 23-ID), Advanced Light Source (8.2.1, 8.2.2) and National Synchrotron Light Source (X-25, X-29A). We are also grateful to J. Berry for help in hybridoma sequencing, B. Bowman for crystallographic advice, E. Gouaux for sharing information about an APC homologue, and P. DeWeer, D. P. Krummel, H. H. Lim, K. Piasta and J. Robertson for suggestions on the manuscript.

Author Contributions Experiments were carried out and diffraction data collected by Y.F., H.J., T.S., L.K.-P., F.W., C.W. and C.M. Data were analysed by Y.F., H.J., Y.X. and C.M. The manuscript was prepared by Y.F., H.J., Y.X. and C.M.

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Correspondence to Christopher Miller.

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This file contains Supplementary Table S1 and Supplementary Figures S1-S3 with Legends. (PDF 481 kb)

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Fang, Y., Jayaram, H., Shane, T. et al. Structure of a prokaryotic virtual proton pump at 3.2 Å resolution. Nature 460, 1040–1043 (2009). https://doi.org/10.1038/nature08201

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