Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Letter
  • Published:

Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP

Nature volume 490, pages 126–130 (2012)Cite this article

Subjects

Abstract

Betaine and Na+ symport has been extensively studied in the osmotically regulated transporter BetP from Corynebacterium glutamicum, a member of the betaine/choline/carnitine transporter family, which shares the conserved LeuT-like fold of two inverted structural repeats1. BetP adjusts its transport activity by sensing the cytoplasmic K+ concentration as a measure for hyperosmotic stress via the osmosensing carboxy-terminal domain2,3. BetP needs to be in a trimeric state for communication between individual protomers through several intratrimeric interaction sites4. Recently, crystal structures of inward-facing BetP trimers have contributed to our understanding of activity regulation on a molecular level5,6. Here we report new crystal structures, which reveal two conformationally asymmetric BetP trimers7, capturing among them three distinct transport states. We observe a total of four new conformations at once: an outward-open apo and an outward-occluded apo state, and two closed transition states—one in complex with betaine and one substrate-free. On the basis of these new structures, we identified local and global conformational changes in BetP that underlie the molecular transport mechanism, which partially resemble structural changes observed in other sodium-coupled LeuT-like fold transporters, but show differences we attribute to the osmolytic nature of betaine, the exclusive substrate specificity and the regulatory properties of BetP.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

Figure 1: Conformational states and substrate-binding sites observed in BetP and BetP(G153D) asymmetric trimers.
Figure 2: Conformational changes during the alternating-access cycle.
Figure 3: Opening and closing of the periplasmic and cytoplasmic gates in BetP.
Figure 4: Conformational changes of the sodium-binding sites.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Coordinates and structure factors for the structures presented here have been deposited in the Protein Data Bank under accession 4DOJ and 4AIN.

References

  1. Ziegler, C., Bremer, E. & Kramer, R. The BCCT family of carriers: from physiology to crystal structure. Mol. Microbiol. 78, 13–34 (2010)

    CAS  PubMed  Google Scholar 

  2. Schiller, D., Rubenhagen, R., Kramer, R. & Morbach, S. The C-terminal domain of the betaine carrier BetP of Corynebacterium glutamicum is directly involved in sensing K+ as an osmotic stimulus. Biochemistry 43, 5583–5591 (2004)

    Article  CAS  Google Scholar 

  3. Rubenhagen, R., Morbach, S. & Kramer, R. The osmoreactive betaine carrier BetP from Corynebacterium glutamicum is a sensor for cytoplasmic K+. EMBO J. 20, 5412–5420 (2001)

    Article  CAS  Google Scholar 

  4. Perez, C., Khafizov, K., Forrest, L. R., Kramer, R. & Ziegler, C. The role of trimerization in the osmoregulated betaine transporter BetP. EMBO Rep. 12, 804–810 (2011)

    Article  CAS  Google Scholar 

  5. Ressl, S., Terwisscha van Scheltinga, A. C., Vonrhein, C., Ott, V. & Ziegler, C. Molecular basis of transport and regulation in the Na+/betaine symporter BetP. Nature 458, 47–52 (2009)

    Article  ADS  CAS  Google Scholar 

  6. Perez, C. et al. Substrate specificity and ion coupling in the Na+/betaine symporter BetP. EMBO J. 30, 1221–1229 (2011)

    Article  CAS  Google Scholar 

  7. Tsai, C. J. et al. Structural asymmetry in a trimeric Na+/betaine symporter, BetP, from Corynebacterium glutamicum. J. Mol. Biol. 407, 368–381 (2011)

    Article  CAS  Google Scholar 

  8. Fang, Y. et al. Structure of a prokaryotic virtual proton pump at 3.2 Å resolution. Nature 460, 1040–1043 (2009)

    Article  ADS  CAS  Google Scholar 

  9. Krishnamurthy, H. & Gouaux, E. X-ray structures of LeuT in substrate-free outward-open and apo inward-open states. Nature 481, 469–474 (2012)

    Article  ADS  CAS  Google Scholar 

  10. Shimamura, T. et al. Molecular basis of alternating access membrane transport by the sodium-hydantoin transporter Mhp1. Science 328, 470–473 (2010)

    Article  ADS  CAS  Google Scholar 

  11. Gärtner, R. M., Perez, C., Koshy, C. & Ziegler, C. Role of bundle helices in a regulatory crosstalk in the trimeric betaine transporter BetP. J. Mol. Biol. 414, 327–336 (2011)

    Article  Google Scholar 

  12. Wetzel, K. J., Bjorge, D. & Schwan, W. R. Mutational and transcriptional analyses of the Staphylococcus aureus low-affinity proline transporter OpuD during in vitro growth and infection of murine tissues. FEMS Immunol. Med. Microbiol. 61, 346–355 (2011)

    Article  CAS  Google Scholar 

  13. Bourot, S. et al. Glycine betaine-assisted protein folding in a lysA mutant of Escherichia coli. J. Biol. Chem. 275, 1050–1056 (2000)

    Article  CAS  Google Scholar 

  14. Zhao, Y. et al. Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature 465, 188–193 (2010)

    Article  ADS  CAS  Google Scholar 

  15. Shi, L. & Weinstein, H. Conformational rearrangements to the intracellular open states of the LeuT and ApcT transporters are modulated by common mechanisms. Biophys. J. 99, L103–L105 (2010)

    Article  CAS  Google Scholar 

  16. Watanabe, A. et al. The mechanism of sodium and substrate release from the binding pocket of vSGLT. Nature 468, 988–991 (2010)

    Article  ADS  CAS  Google Scholar 

  17. Hunte, C. et al. Structure of a Na+/H+ antiporter and insights into mechanism of action and regulation by pH. Nature 435, 1197–1202 (2005)

    Article  ADS  CAS  Google Scholar 

  18. Yamashita, A., Singh, S. K., Kawate, T., Jin, Y. & Gouaux, E. Crystal structure of a bacterial homologue of Na+/Cl−-dependent neurotransmitter transporters. Nature 437, 215–223 (2005)

    Article  ADS  CAS  Google Scholar 

  19. Ziegler, C. et al. Projection structure and oligomeric state of the osmoregulated sodium/glycine betaine symporter BetP of Corynebacterium glutamicum. J. Mol. Biol. 337, 1137–1147 (2004)

    Article  CAS  Google Scholar 

  20. Ott, V., Koch, J., Spate, K., Morbach, S. & Kramer, R. Regulatory properties and interaction of the C- and N-terminal domains of BetP, an osmoregulated betaine transporter from Corynebacterium glutamicum. Biochemistry 47, 12208–12218 (2008)

    Article  CAS  Google Scholar 

  21. Ge, L., Perez, C., Waclawska, I., Ziegler, C. & Muller, D. J. Locating an extracellular K+-dependent interaction site that modulates betaine-binding of the Na+-coupled betaine symporter BetP. Proc. Natl Acad. Sci. USA 108, E890–E898 (2011)

    Article  ADS  CAS  Google Scholar 

Download references

Acknowledgements

We thank L. Forrest and R. Krämer for careful reading of the manuscript and suggestions and discussions. This work was supported by the International Max-Planck Research School (C.K. and C.P.), and by the DFG (German Research Foundation), Collaborative Research Center 807 “Transport and Communication across Biological Membranes” (C.Z.).

Author information

Author notes

  1. Camilo Perez and Caroline Koshy: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Structural Biology, Max-Planck Institute of Biophysics, D-60438 Frankfurt am Main, Germany

    Camilo Perez, Caroline Koshy, Özkan Yildiz & Christine Ziegler

  2. Institute of Biophysics and Biophysical Chemistry, University of Regensburg, D-93053 Regensburg, Germany,

    Christine Ziegler

Authors
  1. Camilo Perez
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Caroline Koshy
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Özkan Yildiz
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Christine Ziegler
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

C.P. performed mutations, activity and binding measurements in cells and proteoliposomes, crystallization, collection and processing of data for PDB accession 4DOJ; C.K. performed crystallization for PDB accession 4AIN; C.K. and Ö.Y. performed collection and processing of data for PDB accession 4AIN; C.P., C.K. and C.Z. analysed the data; C.Z. directed the research; and C.P. and C.Z. wrote the manuscript.

Corresponding author

Correspondence to Christine Ziegler.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Methods, a Supplementary Discussion, Supplementary Tables 1-3, Supplementary Figures 1-10, a legend for Supplementary Movie 1 and Supplementary References. (PDF 6018 kb)

Supplementary Movie 1

The movie represents structural morphs of the conformational changes in BetP during transition from the outward-open to closed and inward-open states – see Supplementary Information file for full legend. (MP4 30132 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Perez, C., Koshy, C., Yildiz, Ö. et al. Alternating-access mechanism in conformationally asymmetric trimers of the betaine transporter BetP. Nature 490, 126–130 (2012). https://doi.org/10.1038/nature11403

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature11403

This article is cited by

Comments

By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing