Skip to main content

Thank you for visiting 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.

Structural insights into amino acid binding and gene control by a lysine riboswitch


In bacteria, the intracellular concentration of several amino acids is controlled by riboswitches1,2,3,4. One of the important regulatory circuits involves lysine-specific riboswitches, which direct the biosynthesis and transport of lysine and precursors common for lysine and other amino acids1,2,3. To understand the molecular basis of amino acid recognition by riboswitches, here we present the crystal structure of the 174-nucleotide sensing domain of the Thermotoga maritima lysine riboswitch in the lysine-bound (1.9 ångström (Å)) and free (3.1 Å) states. The riboswitch features an unusual and intricate architecture, involving three-helical and two-helical bundles connected by a compact five-helical junction and stabilized by various long-range tertiary interactions. Lysine interacts with the junctional core of the riboswitch and is specifically recognized through shape-complementarity within the elongated binding pocket and through several direct and K+-mediated hydrogen bonds to its charged ends. Our structural and biochemical studies indicate preformation of the riboswitch scaffold and identify conformational changes associated with the formation of a stable lysine-bound state, which prevents alternative folding of the riboswitch and facilitates formation of downstream regulatory elements. We have also determined several structures of the riboswitch bound to different lysine analogues5, including antibiotics, in an effort to understand the ligand-binding capabilities of the lysine riboswitch and understand the nature of antibiotic resistance. Our results provide insights into a mechanism of lysine-riboswitch-dependent gene control at the molecular level, thereby contributing to continuing efforts at exploration of the pharmaceutical and biotechnological potential of riboswitches.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Overall structure and long-range tertiary interactions of the lysine-bound T. maritima riboswitch.
Figure 2: Structure and interactions in the junctional region of the lysine riboswitch.
Figure 3: Interactions of lysine analogues with the riboswitch.
Figure 4: Probing lysine riboswitch tertiary structure.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates of the X-ray structures of the lysine riboswitch bound to ligands have been deposited in the RCSB Protein Data Bank under the following accession codes: lysine, 3DIL; AEC, 3DIG; l-4-oxalysine, 3DJ0; homoarginine, 3DIQ; and iminoethyl-l-lysine, 3DIR. Codes for other structures are: free state, 3DIS; [Ir(NH3)6]3+-soaked, 3DIO; Cs+-soaked, 3DIM; Tl+-soaked, 3DJ2; Mn2+-soaked, 3DIY; K+-anomalous, 3DIX; and Mg2+-free form, 3DIZ.


  1. Sudarsan, N., Wickiser, J. K., Nakamura, S., Ebert, M. S. & Breaker, R. R. An mRNA structure in bacteria that controls gene expression by binding lysine. Genes Dev. 17, 2688–2697 (2003)

    CAS  Article  Google Scholar 

  2. Grundy, F. J., Lehman, S. C. & Henkin, T. M. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc. Natl Acad. Sci. USA 100, 12057–12062 (2003)

    CAS  Article  ADS  Google Scholar 

  3. Rodionov, D. A., Vitreschak, A. G., Mironov, A. A. & Gelfand, M. S. Regulation of lysine biosynthesis and transport genes in bacteria: yet another RNA riboswitch? Nucleic Acids Res. 31, 6748–6757 (2003)

    CAS  Article  Google Scholar 

  4. Mandal, M. et al. A glycine-dependent riboswitch that uses cooperative binding to control gene expression. Science 306, 275–279 (2004)

    CAS  Article  ADS  Google Scholar 

  5. Blount, K. F., Wang, J. X., Lim, J., Sudarsan, N. & Breaker, R. R. Antibacterial lysine analogs that target lysine riboswitches. Nature Chem. Biol. 3, 44–49 (2007)

    CAS  Article  Google Scholar 

  6. Serganov, A. & Patel, D. J. Ribozymes, riboswitches and beyond: regulation of gene expression without proteins. Nature Rev. Genet. 8, 776–790 (2007)

    CAS  Article  Google Scholar 

  7. Nudler, E. & Mironov, A. S. The riboswitch control of bacterial metabolism. Trends Biochem. Sci. 29, 11–17 (2004)

    CAS  Article  Google Scholar 

  8. Winkler, W. C. & Breaker, R. R. Regulation of bacterial gene expression by riboswitches. Annu. Rev. Microbiol. 59, 487–517 (2005)

    CAS  Article  Google Scholar 

  9. Chowdhury, S., Maris, C., Allain, F. H. & Narberhaus, F. Molecular basis for temperature sensing by an RNA thermometer. EMBO J. 25, 2487–2497 (2006)

    CAS  Article  Google Scholar 

  10. Dann, C. E. et al. Structure and mechanism of a metal-sensing regulatory RNA. Cell 130, 878–892 (2007)

    CAS  Article  Google Scholar 

  11. Klein, D. J. & Ferre-D’Amare, A. R. Structural basis of glmS ribozyme activation by glucosamine-6-phosphate. Science 313, 1752–1756 (2006)

    CAS  Article  ADS  Google Scholar 

  12. Cochrane, J. C., Lipchock, S. V. & Strobel, S. A. Structural investigation of the GlmS ribozyme bound to its catalytic cofactor. Chem. Biol. 14, 97–105 (2007)

    CAS  Article  Google Scholar 

  13. Batey, R. T., Gilbert, S. D. & Montange, R. K. Structure of a natural guanine-responsive riboswitch complexed with the metabolite hypoxanthine. Nature 432, 411–415 (2004)

    CAS  Article  ADS  Google Scholar 

  14. Serganov, A. et al. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem. Biol. 11, 1729–1741 (2004)

    CAS  Article  Google Scholar 

  15. Serganov, A., Polonskaia, A., Phan, A. T., Breaker, R. R. & Patel, D. J. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature 441, 1167–1171 (2006)

    CAS  Article  ADS  Google Scholar 

  16. Thore, S., Leibundgut, M. & Ban, N. Structure of the eukaryotic thiamine pyrophosphate riboswitch with its regulatory ligand. Science 312, 1208–1211 (2006)

    CAS  Article  ADS  Google Scholar 

  17. Edwards, T. E. & Ferre-D’Amare, A. R. Crystal structures of the thi-box riboswitch bound to thiamine pyrophosphate analogs reveal adaptive RNA-small molecule recognition. Structure 14, 1459–1468 (2006)

    CAS  Article  Google Scholar 

  18. Montange, R. K. & Batey, R. T. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature 441, 1172–1175 (2006)

    CAS  Article  ADS  Google Scholar 

  19. Gilbert, S. D., Rambo, R. P., Van Tyne, D. & Batey, R. T. Structure of the SAM-II riboswitch bound to S-adenosylmethionine. Nature Struct. Mol. Biol. 15, 177–182 (2008)

    CAS  Article  Google Scholar 

  20. Weixlbaumer, A. et al. Crystal structure of the ribosome recycling factor bound to the ribosome. Nature Struct. Mol. Biol. 14, 733–737 (2007)

    CAS  Article  Google Scholar 

  21. Blouin, S. & Lafontaine, D. A. A loop–loop interaction and a K-turn motif located in the lysine aptamer domain are important for the riboswitch gene regulation control. RNA 13, 1256–1267 (2007)

    CAS  Article  Google Scholar 

  22. Correll, C. C., Freeborn, B., Moore, P. B. & Steitz, T. A. Metals, motifs, and recognition in the crystal structure of a 5S rRNA domain. Cell 91, 705–712 (1997)

    CAS  Article  Google Scholar 

  23. Leontis, N. B. & Westhof, E. The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure. RNA 4, 1134–1153 (1998)

    CAS  Article  Google Scholar 

  24. Klein, D. J., Schmeing, T. M., Moore, P. B. & Steitz, T. A. The kink-turn: a new RNA secondary structure motif. EMBO J. 20, 4214–4221 (2001)

    CAS  Article  Google Scholar 

  25. Basu, S. et al. A specific monovalent metal ion integral to the AA platform of the RNA tetraloop receptor. Nature Struct. Biol. 5, 986–992 (1998)

    CAS  Article  Google Scholar 

  26. Feig, A. L. & Uhlenbeck, O. C. in The RNA World Second Edition (eds Gesteland, R. F., Cech, T. R. & Atkins, J. F.) 287–319 (Cold Spring Harbor Laboratory Press, 1999)

    Google Scholar 

  27. Lu, Y., Shevtchenko, T. N. & Paulus, H. Fine-structure mapping of cis-acting control sites in the lysC operon of Bacillus subtilis . FEMS Microbiol. Lett. 92, 23–27 (1992)

    CAS  Article  Google Scholar 

  28. Patte, J. C., Akrim, M. & Mejean, V. The leader sequence of the Escherichia coli lysC gene is involved in the regulation of LysC synthesis. FEMS Microbiol. Lett. 169, 165–170 (1998)

    CAS  Article  Google Scholar 

  29. Ataide, S. F. et al. Mechanisms of resistance to an amino acid antibiotic that targets translation. ACS Chem. Biol. 2, 819–827 (2007)

    CAS  Article  Google Scholar 

  30. de La Fortelle, E. & Bricogne, G. in Methods in Enzymology 472–494 (Academic Press, 1997)

    Google Scholar 

  31. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    CAS  Article  Google Scholar 

  32. Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463 (1999)

    CAS  Article  Google Scholar 

Download references


We thank personnel of beamline X29 at the Brookhaven National Laboratory and beamlines 24-ID-C/E at the Advanced Photon Source, Argonne National Laboratory, funded by the US Department of Energy. We thank O. Ouerfelli for the synthesis of iridium hexamine. D.J.P. was supported by funds from the National Institutes of Health.

Author Contributions L.H. crystallized the T. maritima lysine riboswitch; A.S. determined the structures and was assisted by L.H. during refinement; A.S. and L.H. performed biochemical experiments; and A.S. and D.J.P. wrote the manuscript. All authors discussed the results and commented on the manuscript.

Author information

Authors and Affiliations


Corresponding authors

Correspondence to Alexander Serganov or Dinshaw J. Patel.

Supplementary information

Supplementary Information

The file contains Supplementary Figures 1-17 and Legends, Supplementary Tables 1-3 and Supplementary Notes (PDF 8637 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Serganov, A., Huang, L. & Patel, D. Structural insights into amino acid binding and gene control by a lysine riboswitch. Nature 455, 1263–1267 (2008).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

Further reading


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.


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