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Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori

Nature volume 493, pages 255–258 (2013)Cite this article

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Abstract

Half the world’s population is chronically infected with Helicobacter pylori1, causing gastritis, gastric ulcers and an increased incidence of gastric adenocarcinoma2. Its proton-gated inner-membrane urea channel, HpUreI, is essential for survival in the acidic environment of the stomach3. The channel is closed at neutral pH and opens at acidic pH to allow the rapid access of urea to cytoplasmic urease4. Urease produces NH3 and CO2, neutralizing entering protons and thus buffering the periplasm to a pH of roughly 6.1 even in gastric juice at a pH below 2.0. Here we report the structure of HpUreI, revealing six protomers assembled in a hexameric ring surrounding a central bilayer plug of ordered lipids. Each protomer encloses a channel formed by a twisted bundle of six transmembrane helices. The bundle defines a previously unobserved fold comprising a two-helix hairpin motif repeated three times around the central axis of the channel, without the inverted repeat of mammalian-type urea transporters. Both the channel and the protomer interface contain residues conserved in the AmiS/UreI superfamily, suggesting the preservation of channel architecture and oligomeric state in this superfamily. Predominantly aromatic or aliphatic side chains line the entire channel and define two consecutive constriction sites in the middle of the channel. Mutation of Trp 153 in the cytoplasmic constriction site to Ala or Phe decreases the selectivity for urea in comparison with thiourea, suggesting that solute interaction with Trp 153 contributes specificity. The previously unobserved hexameric channel structure described here provides a new model for the permeation of urea and other small amide solutes in prokaryotes and archaea.

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Figure 1: The Hp UreI urea channel hexamer.
Figure 2: Residues lining the channel.
Figure 3: Structural conservation of a two-helical hairpin motif.
Figure 4: Views of the Hp UreI channel traversed by urea.

Accession codes

Primary accessions

Protein Data Bank

Change history

  • 09 January 2013

    In the Fig. 4c legend, amino acid numbering of Phe 84 was corrected.

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Acknowledgements

We thank the following for assistance with X-ray data collection at the Stanford Synchrotron Radiation Lightsource (T. Doukov), the Advanced Photon Source (D. Cascio & R. Rajashankar), the Advanced Light Source (J. Nix) and the Swiss Light Source (C. Schulze-Briese). We also thank J. Whitelegge for mass spectrometry characterization of potential heavy atom derivatives; D. R. Scott for the urease assays; B. Hirayama for advice on the oocyte experiments; N. Echols and T. Terwilliger for assistance with the development version of the program Phenix; A. Murzin for fold characterization; T. Silkov for pseudosymmetry analysis; and D. R. Scott, F. Tombola, V. De Souza, K. Luecke, S. Luecke and J. Lanyi for general suggestions. This work was supported by National Institutes of Health (NIH) grants R01AI78000 and P30CA062203, National Cancer Institute institutional training grant 5 T32 CA9054-34, the University of California Irvine Center for Biomembrane Systems (H.L.), NIH grants R01DK53462 and R01DK58333 (G.S.) and the US Veterans Administration (G.S). Portions of this research were performed at the Stanford Synchrotron Radiation Lightsource, a Directorate of SLAC National Accelerator Laboratory and an Office of Science User Facility operated for the US Department of Energy (DOE) Office of Science by Stanford University. The Stanford Synchrotron Radiation Lightsource Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the HIN, National Center for Research Resources, Biomedical Technology Program (P41RR001209) and the National Institute of General Medical Sciences.

Author information

Author notes

  1. Reginald McNulty

    Present address: Present address: Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.,

  2. David Strugatsky, Reginald McNulty and Keith Munson: These authors contributed equally to this work.

Authors and Affiliations

  1. David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, 90073, California, USA

    David Strugatsky, Keith Munson & George Sachs

  2. Department of Molecular Biology and Biochemistry, University of California, Irvine, 92697-3900, California, USA

    Reginald McNulty, Chiung-Kuang Chen & Hartmut Luecke

  3. Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, 94025, California, USA

    S. Michael Soltis

  4. Center for Biomembrane Systems, University of California, Irvine, 92697, California, USA

    Hartmut Luecke

  5. Department of Physiology and Biophysics, University of California, Irvine, 92697, California, USA

    Hartmut Luecke

  6. Department of Computer Science, University of California, Irvine, 92697, California, USA

    Hartmut Luecke

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Contributions

G.S. and H.L. contributed to the design of the project. D.S. and K.M. expressed, purified and crystallized HpUreI. D.S. conducted the oocyte uptake measurements. C.-K.C. helped with expression and native gels. R.M. and H.L. performed the crystallographic experiments and analysis of data. S.M.S. assisted with aspects of phasing. G.S. and H.L. were responsible for overall project management and wrote the manuscript with K.M.

Corresponding authors

Correspondence to George Sachs or Hartmut Luecke.

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Competing interests

The authors declare no competing financial interests.

Additional information

The coordinates and structure factors are deposited at the Protein Data Bank under PDB code 3UX4.

Supplementary information

Supplementary Information

This file contains Supplementary Text and Figures 1-13, Supplementary Tables 1-2 and Supplementary References. (PDF 7240 kb)

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Strugatsky, D., McNulty, R., Munson, K. et al. Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori. Nature 493, 255–258 (2013). https://doi.org/10.1038/nature11684

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