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Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4 Å

Nature volume 483, pages 489–493 (2012)Cite this article

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Abstract

Nucleosides are required for DNA and RNA synthesis, and the nucleoside adenosine has a function in a variety of signalling processes1,2. Transport of nucleosides across cell membranes provides the major source of nucleosides in many cell types and is also responsible for the termination of adenosine signalling. As a result of their hydrophilic nature, nucleosides require a specialized class of integral membrane proteins, known as nucleoside transporters (NTs), for specific transport across cell membranes. In addition to nucleosides, NTs are important determinants for the transport of nucleoside-derived drugs across cell membranes3,4,5. A wide range of nucleoside-derived drugs, including anticancer drugs (such as Ara-C and gemcitabine) and antiviral drugs (such as zidovudine and ribavirin), have been shown to depend, at least in part, on NTs for transport across cell membranes4,6,7,8,9,10,11,12,13. Concentrative nucleoside transporters, members of the solute carrier transporter superfamily SLC28, use an ion gradient in the active transport of both nucleosides and nucleoside-derived drugs against their chemical gradients. The structural basis for selective ion-coupled nucleoside transport by concentrative nucleoside transporters is unknown. Here we present the crystal structure of a concentrative nucleoside transporter from Vibrio cholerae in complex with uridine at 2.4 Å. Our functional data show that, like its human orthologues, the transporter uses a sodium-ion gradient for nucleoside transport. The structure reveals the overall architecture of this class of transporter, unravels the molecular determinants for nucleoside and sodium binding, and provides a framework for understanding the mechanism of nucleoside and nucleoside drug transport across cell membranes.

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Figure 1: vcCNT is a Na + -coupled nucleoside transporter with a trimeric architecture.
Figure 2: Topology and fold of the vcCNT protomer.
Figure 3: Nucleoside-binding site and Na + -binding site.
Figure 4: Hypothetical mechanism of nucleoside transport.

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure are deposited in the Protein Data Bank under accession code 3TIJ.

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Acknowledgements

Data for this study were collected at beamlines SER-CAT BM22/ID22 and NE-CAT ID 24-C at the Advanced Photon Source. We thank R. MacKinnon and J. Butterwick for critical reading; R. Lefkowitz and A. Shukla for providing access and technical support for the radioactive flux assay; S. Lockless for advice on experiments; and C. Pemble for help with remote data collection. This work was supported by start-up funds from the Duke University Medical Center, the McKnight Endowment Fund for Neuroscience, the Alfred P. Sloan Foundation, the Klingenstein Fund, the Mallinckrodt foundation, the Basil O’Connor Starter Scholar Research Award 5-FY10-473 from the March of Dimes Foundation, and the National Institutes of Health Director’s New Innovator Award 1 DP2 OD008380-01 (all to S.-Y.L.).

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Authors and Affiliations

  1. Department of Biochemistry and Ion Channel Research Unit, Duke University Medical Center, 2 Genome Court, Durham, North Carolina 27710, USA,

    Zachary Lee Johnson, Cheom-Gil Cheong & Seok-Yong Lee

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  3. Seok-Yong Lee
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Contributions

Z.J. expressed, purified and crystallized vcCNT. Z.J. performed radioactive flux and crosslinking experiments. C.-G.C. participated in part of the vcCNT crystallization and generated mutants for crystallization and functional studies. Z.J. and S.-Y.L. collected and processed the data, solved the structure, and wrote the paper. S.-Y.L. designed the study. All authors discussed the results and commented on the manuscript.

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Correspondence to Seok-Yong Lee.

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The authors declare no competing financial interests.

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This file contains Supplementary Table 1, Supplementary Figures 1-7, a Supplementary Discussion and additional references. (PDF 7882 kb)

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Johnson, Z., Cheong, CG. & Lee, SY. Crystal structure of a concentrative nucleoside transporter from Vibrio cholerae at 2.4 Å. Nature 483, 489–493 (2012). https://doi.org/10.1038/nature10882

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