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Crystal structure of a potassium ion transporter, TrkH

Nature volume 471, pages 336–340 (2011)Cite this article

Abstract

The TrkH/TrkG/KtrB proteins mediate K+ uptake in bacteria and probably evolved from simple K+ channels by multiple gene duplications or fusions. Here we present the crystal structure of a TrkH from Vibrio parahaemolyticus. TrkH is a homodimer, and each protomer contains an ion permeation pathway. A selectivity filter, similar in architecture to those of K+ channels but significantly shorter, is lined by backbone and side-chain oxygen atoms. Functional studies showed that TrkH is selective for permeation of K+ and Rb+ over smaller ions such as Na+ or Li+. Immediately intracellular to the selectivity filter are an intramembrane loop and an arginine residue, both highly conserved, which constrict the permeation pathway. Substituting the arginine with an alanine significantly increases the rate of K+ flux. These results reveal the molecular basis of K+ selectivity and suggest a novel gating mechanism for this large and important family of membrane transport proteins.

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Figure 1: Function and structure of VpTrkH.
Figure 2: The VpTrkH pore.
Figure 3: Selectivity filter of VpTrkH.
Figure 4: Constriction formed by Arg 468 and the intramembrane loop.

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors are deposited in Protein Data Bank under accession number 3PJZ.

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Acknowledgements

Data for this study were measured at beamlines X4A, X4C, X25 and X29 of the National Synchrotron Light Source and the NE-CAT 24ID-C and E at the Advanced Photon Source. This work was supported by the U.S. National Institutes of Health (grants HL086392, DK088057 and GM05026-sub0007 to M.Z.) and the American Heart Association (0630148N to M.Z.). M.Z is a Pew Scholar in Biomedical Sciences. The New York Consortium on Membrane Protein Structure central facility is supported by grant GM05026 to W.A.H. as part of the Protein Structure Initiative (PSI-2) established by the National Institute of General Medical Sciences. We thank B. Honig for support, K. Jung for providing E. coli LB650, and J. Morais-Cabral, S.-Y. Lee, H. R. Guy, C. L. Slayman and E. P. Bakker for discussions and comments on the manuscript. M.Z. is grateful to R. MacKinnon for advice and support throughout the project.

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Author notes

  1. Yu Cao, Xiangshu Jin and Hua Huang: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Physiology & Cellular Biophysics, College of Physicians and Surgeons, Columbia University, 630 West 168th Street, New York, 10032, New York, USA

    Yu Cao, Hua Huang, Elena J. Levin, Venkataraman Kabaleeswaran, Yaping Pan, Jun Weng & Ming Zhou

  2. Department of Biochemistry and Molecular Biophysics, Center for Computational Biology and Bioinformatics, Howard Hughes Medical Institute, Columbia University, 1130 St Nicholas Avenue, Room 815, New York, 10032, New York, USA

    Xiangshu Jin

  3. Department of Physiology and Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, 75390, Texas, USA

    Mehabaw Getahun Derebe, Sheng Ye & Youxing Jiang

  4. New York Consortium on Membrane Protein Structure, New York Structural Biology Center, 89 Convent Avenue, New York, 10027, New York, USA

    Marco Punta, James Love, Brian Kloss, Renato Bruni & Burkhard Rost

  5. Department of Computer Science and Institute for Advanced Study, Technical University of Munich, D-85748 Munich, Germany

    Marco Punta & Burkhard Rost

  6. Center for Molecular Recognition and Department of Psychiatry, Columbia University, 630 West 168th Street, New York, 10032, New York, USA

    Matthias Quick & Jonathan A. Javitch

  7. Division of Molecular Therapeutics, New York State Psychiatric Institute, 1051 Riverside Drive, New York, 10032, New York, USA

    Matthias Quick & Jonathan A. Javitch

  8. Department of Biochemistry and Molecular Biophysics, Howard Hughes Medical Institute, Columbia University, 630 West 168th Street, New York, 10032, New York, USA

    Erik Martinez-Hackert & Wayne A. Hendrickson

  9. Department of Pharmacology, Columbia University, 630 West 168th Street, New York, 10032, New York, USA

    Jonathan A. Javitch

  10. Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Advanced Photon Source, Argonne, 60439, Illinois, USA

    Kanagalaghatta R. Rajashankar

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Contributions

M.P., J.L., B.R. and W.A.H. identified TrkH/TrkG/KtrB homologues in the database. R.B., B.K. and J.L. cloned and tested expression of the homologues. Y.C., H.H., J.W., E.J.L. and M.Z. scaled up production of proteins, produced and refined VpTrkH crystals, and collected and analysed X-ray diffraction data. X.J., E.J.L. and M.Z. solved and refined the structures. V.K., S.Y. and E.M-H. analysed diffraction data and obtained a partial model in early stages of the project. Y.C., M.G.D., M.Q., Y.P., Y.J., J.A.J. and M.Z. characterized VpTrkH function. K.R.R. and W.A.H. advised on data collection and crystallography. E.J.L. and M.Z wrote the manuscript with inputs from all authors.

Corresponding author

Correspondence to Ming Zhou.

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Cao, Y., Jin, X., Huang, H. et al. Crystal structure of a potassium ion transporter, TrkH. Nature 471, 336–340 (2011). https://doi.org/10.1038/nature09731

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