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.

  • Brief Communication
  • Published:

Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch

Nature Structural & Molecular Biology volume 19, pages 1182–1184 (2012)Cite this article

Subjects

Abstract

Coenzyme B12 has a key role in various enzymatic reactions and controls expression of bacterial genes through riboswitches. Here we report the crystal structure of the Symbiobacterium thermophilum B12 riboswitch bound to its ligand adenosylcobalamin. The riboswitch forms a unique junctional structure with a large ligand-binding pocket tailored for specific recognition of the adenosyl moiety and flanked by structural elements that stabilize the regulatory region and enable control of gene expression.

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: Overall structure and schematics of the S. thermophilum AdoCbl riboswitch.
Figure 2: Structure and interactions within and around the junctional region.
Figure 3: Riboswitch stabilization and molecular mechanism of function.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

References

  1. Lundrigan, M.D., Koster, W. & Kadner, R.J. Proc. Natl. Acad. Sci. USA 88, 1479–1483 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Nou, X. & Kadner, R.J. Proc. Natl. Acad. Sci. USA 97, 7190–7195 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Ravnum, S. & Andersson, D.I. Mol. Microbiol. 39, 1585–1594 (2001).

    Article  CAS  PubMed  Google Scholar 

  4. Mironov, A.S. et al. Cell 111, 747–756 (2002).

    Article  CAS  PubMed  Google Scholar 

  5. Nahvi, A. et al. Chem. Biol. 9, 1043 (2002).

    Article  CAS  PubMed  Google Scholar 

  6. Winkler, W., Nahvi, A. & Breaker, R.R. Nature 419, 952–956 (2002).

    Article  CAS  PubMed  Google Scholar 

  7. Nahvi, A., Barrick, J.E. & Breaker, R.R. Nucleic Acids Res. 32, 143–150 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Rodionov, D.A., Vitreschak, A.G., Mironov, A.A. & Gelfand, M.S. J. Biol. Chem. 278, 41148–41159 (2003).

    Article  CAS  PubMed  Google Scholar 

  9. Jaeger, L., Verzemnieks, E.J. & Geary, C. Nucleic Acids Res. 37, 215–230 (2009).

    Article  CAS  PubMed  Google Scholar 

  10. Serganov, A., Huang, L. & Patel, D.J. Nature 458, 233–237 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Serganov, A., Huang, L. & Patel, D.J. Nature 455, 1263–1267 (2008).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Gallo, S., Oberhuber, M., Sigel, R.K. & Krautler, B. ChemBioChem 9, 1408–1414 (2008).

    Article  CAS  PubMed  Google Scholar 

  13. Sussman, D., Nix, J.C. & Wilson, C. Nat. Struct. Biol. 7, 53–57 (2000).

    Article  CAS  PubMed  Google Scholar 

  14. Borovok, I., Gorovitz, B., Schreiber, R., Aharonowitz, Y. & Cohen, G. J. Bacteriol. 188, 2512–2520 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Warner, D.F., Savvi, S., Mizrahi, V. & Dawes, S.S. J. Bacteriol. 189, 3655–3659 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  16. Loh, E. et al. Cell 139, 770–779 (2009).

    Article  CAS  PubMed  Google Scholar 

  17. Serganov, A. et al. Eur. J. Biochem. 246, 291–300 (1997).

    Article  CAS  PubMed  Google Scholar 

  18. Pikovskaya, O., Serganov, A.A., Polonskaia, A., Serganov, A. & Patel, D.J. Methods Mol. Biol. 540, 115–128 (2009).

    Article  CAS  PubMed  Google Scholar 

  19. Adams, P.D. et al. Acta Crystallogr. D Biol. Crystallogr. 66, 213–221 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Emsley, P., Lohkamp, B., William, G., Scott, W.G. & Cowtan, K. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

We thank personnel of beamlines X25 and X4C at the Brookhaven National Laboratory funded by the US Department of Energy, O. Ouerfelli (Memorial Sloan-Kettering Cancer Center) for the synthesis of iridium hexamine and E. Wasmuth for initial input into the project. A.S. was supported by funds from the New York University School of Medicine.

Author information

Authors and Affiliations

  1. Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA

    Alla Peselis & Alexander Serganov

Authors
  1. Alla Peselis
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Alexander Serganov
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.P. crystallized the AdoCbl riboswitch, A.S. determined the crystal structure. A.P. and A.S. wrote the manuscript.

Corresponding author

Correspondence to Alexander Serganov.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5 and Supplementary Table 1 (PDF 5382 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Peselis, A., Serganov, A. Structural insights into ligand binding and gene expression control by an adenosylcobalamin riboswitch. Nat Struct Mol Biol 19, 1182–1184 (2012). https://doi.org/10.1038/nsmb.2405

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.2405

This article is cited by

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