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Structure and mechanism of a pentameric formate channel

Nature Structural & Molecular Biology volume 17, pages 31–37 (2010)Cite this article

Abstract

Formate transport across the inner membrane is a critical step in anaerobic bacterial respiration. Members of the formate/nitrite transport protein family function to shuttle substrate across the cytoplasmic membrane. In bacterial pathogens, the nitrite transport protein is involved in protecting bacteria from peroxynitrite released by host macrophages. We have determined the 2.13-Å structure of the formate channel FocA from Vibrio cholerae, which reveals a pentamer in which each monomer possesses its own substrate translocation pore. Unexpectedly, the fold of the FocA monomer resembles that found in water and glycerol channels. The selectivity filter in FocA consists of a cytoplasmic slit and a central constriction ring. A 2.5-Å high-formate structure shows two formate ions bound to the cytoplasmic slit via both hydrogen bonding and van der Waals interactions, providing a structural basis for the substrate selectivity of the channel.

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Figure 1: Characterization of the FocA protein from V. cholerae.
Figure 2: Overall structure and transmembrane topology of FocA monomer in the low-formate crystal form, represented by monomer A.
Figure 3: Different configurations of the Ω loop that connects TM2a and TM3 in different FocA monomers, both from the low-formate structure.
Figure 4: Pore structure in the FocA monomer at low formate concentration.
Figure 5: FocA selectivity structure and interactions with formate.

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Acknowledgements

We are grateful to W.A. Hendrickson for support, to M. Punta and B. Rost for bioinformatics analysis of membrane transporters, to B. Kloss for assistance in cloning, and to the staff at beamlines X25 and X29 of the National Synchrotron Light Source in the Brookhaven National Laboratory for assistance in X-ray diffraction experiments. We thank B. Czyzewski, Y. Fujiyoshi, N. K. Karpowich, C.J. Law, X.D. Li, J.J. Marden, R.L. Mancusso, H. Sui, J. Wu, R.M. Xu, N. Unwin, T. Walz, M. Zhou and Z. Zhou for participating synchrotron trips and helpful discussions. This work was financially supported by the Protein Structure Initiative II of the US National Institutes of Health (U54GM075026 to W.A. Hendrickson) and by US National Institute of Diabetes and Digestive and Kidney Diseases (R01-073973 to D.-N.W.). A.B.W. was partially supported by a predoctoral fellowship from the US National Institutes of Health–New York University Graduate Partnership Program in Structural Biology.

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Authors and Affiliations

  1. The Helen L. and Martin S. Kimmel Center for Biology and Medicine at the Skirball Institute of Biomolecular Medicine, New York University School of Medicine, New York, New York, USA

    Andrew B Waight & Da-Neng Wang

  2. Department of Cell Biology, New York University School of Medicine, New York, New York, USA

    Andrew B Waight & Da-Neng Wang

  3. Structural Biology Graduate Program, New York University School of Medicine, New York, New York, USA

    Andrew B Waight

  4. New York Structural Biology Center, Park Building, New York, New York, USA

    James Love

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  1. Andrew B Waight
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A.B.W. expressed, purified, crystallized and solved the structure of FocA and functionally characterized the protein. J.L. provided the initial clone and measured the protein oligomeric state. D.-N.W. performed electron microscopy. A.B.W. and D.-N.W. wrote the manuscript.

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Correspondence to Da-Neng Wang.

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Waight, A., Love, J. & Wang, DN. Structure and mechanism of a pentameric formate channel. Nat Struct Mol Biol 17, 31–37 (2010). https://doi.org/10.1038/nsmb.1740

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