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:

Structure of the LexA–DNA complex and implications for SOS box measurement

Nature volume 466, pages 883–886 (2010)Cite this article

Subjects

Abstract

The eubacterial SOS system is a paradigm of cellular DNA damage and repair, and its activation can contribute to antibiotic resistance1,2,3. Under normal conditions, LexA represses the transcription of many DNA repair proteins by binding to SOS ‘boxes’ in their operators. Under genotoxic stress, accumulating complexes of RecA, ATP and single-stranded DNA (ssDNA) activate LexA for autocleavage. To address how LexA recognizes its binding sites, we determined three crystal structures of Escherichia coli LexA in complex with SOS boxes. Here we report the structure of these LexA–DNA complexes. The DNA-binding domains of the LexA dimer interact with the DNA in the classical fashion of a winged helix–turn–helix motif. However, the wings of these two DNA-binding domains bind to the same minor groove of the DNA. These wing–wing contacts may explain why the spacing between the two half-sites of E. coli SOS boxes is invariant.

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

Access options

Buy this article

  • Purchase on SpringerLink
  • Instant access to full article PDF
Buy now

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

Figure 1: Overall structure of the E. coli LexA–DNA complex.
Figure 2: Binding of the E. coli LexA–DNA complex.

Similar content being viewed by others

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Atomic coordinates and structure factor files have been deposited with the Protein Data Bank under the accession codes 3JSO (A22), 3JSP (B22) and 3K3R (C29).

References

  1. Walker, G. C. Inducible DNA repair systems. Annu. Rev. Biochem. 54, 425–457 (1985)

    Article  CAS  Google Scholar 

  2. Shinagawa, H. SOS response as an adaptive response to DNA damage in prokaryotes. EXS 77, 221–235 (1996)

    CAS  PubMed  Google Scholar 

  3. Erill, I., Campoy, S. & Barbe, J. Aeons of distress: an evolutionary perspective on the bacterial SOS response. FEMS Microbiol. Rev. 31, 637–656 (2007)

    Article  CAS  Google Scholar 

  4. Luo, Y. et al. Crystal structure of LexA: a conformational switch for regulation of self-cleavage. Cell 106, 585–594 (2001)

    Article  CAS  Google Scholar 

  5. Neher, S. B., Flynn, J. M., Sauer, R. T. & Baker, T. A. Latent ClpX-recognition signals ensure LexA destruction after DNA damage. Genes Dev. 17, 1084–1089 (2003)

    Article  CAS  Google Scholar 

  6. Hurstel, S., Granger-Schnarr, M. & Schnarr, M. Contacts between the LexA repressor–or its DNA-binding domain–and the backbone of the recA operator DNA. EMBO J. 7, 269–275 (1988)

    Article  CAS  Google Scholar 

  7. Knegtel, R. M. et al. A model for the LexA repressor DNA complex. Proteins 21, 226–236 (1995)

    Article  CAS  Google Scholar 

  8. Butala, M., Zgur-Bertok, D. & Busby, S. J. The bacterial LexA transcriptional repressor. Cell. Mol. Life Sci. 66, 82–93 (2009)

    Article  CAS  Google Scholar 

  9. Schultz, S. C., Shields, G. C. & Steitz, T. A. Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees. Science 253, 1001–1007 (1991)

    Article  ADS  CAS  Google Scholar 

  10. Hong, M., Fuangthong, M., Helmann, J. D. & Brennan, R. G. Structure of an OhrR-ohrA operator complex reveals the DNA binding mechanism of the MarR family. Mol. Cell 20, 131–141 (2005)

    Article  CAS  Google Scholar 

  11. Thliveris, A. T., Little, J. W. & Mount, D. W. Repression of the E. coli recA gene requires at least two LexA protein monomers. Biochimie 73, 449–456 (1991)

    Article  CAS  Google Scholar 

  12. Mohana-Borges, R. et al. LexA repressor forms stable dimers in solution. The role of specific DNA in tightening protein–protein interactions. J. Biol. Chem. 275, 4708–4712 (2000)

    Article  CAS  Google Scholar 

  13. Oertel-Buchheit, P., Porte, D., Schnarr, M. & Granger-Schnarr, M. Isolation and characterization of LexA mutant repressors with enhanced DNA binding affinity. J. Mol. Biol. 225, 609–620 (1992)

    Article  CAS  Google Scholar 

  14. Groban, E. S. et al. Binding of the Bacillus subtilis LexA protein to the SOS operator. Nucleic Acids Res. 33, 6287–6295 (2005)

    Article  ADS  CAS  Google Scholar 

  15. Butala, M., Hodoscek, M., Anderluh, G., Podlesek, Z. & Zgur-Bertok, D. Intradomain LexA rotation is a prerequisite for DNA binding specificity. FEBS Lett. 581, 4816–4820 (2007)

    Article  CAS  Google Scholar 

  16. Giese, K. C., Michalowski, C. B. & Little, J. W. RecA-dependent cleavage of LexA dimers. J. Mol. Biol. 377, 148–161 (2008)

    Article  CAS  Google Scholar 

  17. Thliveris, A. T. & Mount, D. W. Genetic identification of the DNA binding domain of Escherichia coli LexA protein. Proc. Natl Acad. Sci. USA 89, 4500–4504 (1992)

    Article  ADS  CAS  Google Scholar 

  18. Fernandez De Henestrosa, A. R. et al. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35, 1560–1572 (2000)

    Article  CAS  Google Scholar 

  19. Wade, J. T., Reppas, N. B., Church, G. M. & Struhl, K. Genomic analysis of LexA binding reveals the permissive nature of the Escherichia coli genome and identifies unconventional target sites. Genes Dev. 19, 2619–2630 (2005)

    Article  CAS  Google Scholar 

  20. Oertel-Buchheit, P., Lamerichs, R. M., Schnarr, M. & Granger-Schnarr, M. Genetic analysis of the LexA repressor: isolation and characterization of LexA(Def) mutant proteins. Mol. Gen. Genet. 223, 40–48 (1990)

    Article  CAS  Google Scholar 

  21. Dumoulin, P., Oertel-Buchheit, P., Granger-Schnarr, M. & Schnarr, M. Orientation of the LexA DNA-binding motif on operator DNA as inferred from cysteine-mediated phenyl azide crosslinking. Proc. Natl Acad. Sci. USA 90, 2030–2034 (1993)

    Article  ADS  CAS  Google Scholar 

  22. Lewis, L. K., Harlow, G. R., Gregg-Jolly, L. A. & Mount, D. W. Identification of high affinity binding sites for LexA which define new DNA damage-inducible genes in Escherichia coli. J. Mol. Biol. 241, 507–523 (1994)

    Article  CAS  Google Scholar 

  23. Koudelka, G. B. & Carlson, P. DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor. Nature 355, 89–91 (1992)

    Article  ADS  CAS  Google Scholar 

  24. Wu, L., Vertino, A. & Koudelka, G. B. Non-contacted bases affect the affinity of synthetic P22 operators for P22 repressor. J. Biol. Chem. 267, 9134–9139 (1992)

    CAS  PubMed  Google Scholar 

  25. Littlefield, O. & Nelson, H. C. A new use for the ‘wing’ of the ‘winged’ helix–turn–helix motif in the HSF–DNA cocrystal. Nature Struct. Biol. 6, 464–470 (1999)

    Article  CAS  Google Scholar 

  26. Garnett, J. A., Marincs, F., Baumberg, S., Stockley, P. G. & Phillips, S. E. Structure and function of the arginine repressor–operator complex from Bacillus subtilis. J. Mol. Biol. 379, 284–298 (2008)

    Article  CAS  Google Scholar 

  27. DeLano, W. L. The PyMOL Molecular Graphics System (DeLano Scientific, 2002)

    Google Scholar 

  28. Kabsch, W. A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. A 32, 922–923 (1976)

    Article  ADS  Google Scholar 

  29. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. & McCammon, J. A. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl Acad. Sci. USA 98, 10037–10041 (2001)

    Article  ADS  CAS  Google Scholar 

  30. Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

    Article  CAS  Google Scholar 

  31. McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Cryst. 40, 658–674 (2007)

    Article  CAS  Google Scholar 

  32. Collaborative Computational Project No. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760–763 (1994)

  33. Vagin, A. & Teplyakov, A. MOLREP: an automated program for molecular replacement. J. Appl. Cryst. 30, 1022–1025 (1997)

    Article  CAS  Google Scholar 

  34. Otwinowski, Z. in Isomorphous Replacement and Anomalous Scattering (eds Wolf, W., Evans, P. R. & Leslie, A. G. W.) 80–85 (The CCP4 Study Weekend, SERC Daresbury Laboratory, 1991)

    Google Scholar 

  35. Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126–2132 (2004)

    Article  Google Scholar 

  36. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A 47, 110–119 (1991)

    Article  Google Scholar 

  37. Brunger, A. T. et al. Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905–921 (1998)

    Article  CAS  Google Scholar 

  38. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283–291 (1993)

    Article  CAS  Google Scholar 

  39. Davis, I. W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–W383 (2007)

    Article  ADS  Google Scholar 

Download references

Acknowledgements

We thank E. Harris and O. Adekeye for help with crystal growth and optimization; Y.-L. C. Leung for advice on DNA-binding assays; S. Montaño and other members of the Rice laboratory for help and discussions; the staffs at beamlines BioCARS 14, SBC 19-ID and 19-BM, and LS-CAT 21-ID-F at the Advanced Photon Source, Argonne National Laboratory, for helping with the synchrotron X-ray data collection. The research is supported in part by National Institutes of Health grant GM058827.

Author information

Author notes

  1. Adrianna P. P. Zhang

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

Authors and Affiliations

  1. Department of Chemistry, The University of Chicago, Chicago, 60637, Illinois, USA

    Adrianna P. P. Zhang

  2. Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, 60637, Illinois, USA

    Ying Z. Pigli & Phoebe A. Rice

Authors
  1. Adrianna P. P. Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Ying Z. Pigli
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Phoebe A. Rice
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

A.P.P.Z. grew the crystals, determined the structure and performed the affinity assays. Y.Z.P. assisted greatly with cloning, protein purification, and crystal screening and optimization. P.R. designed and directed the project and assisted in crystallographic data collection and structure determination. A.P.P.Z. and P.A.R. wrote the manuscript.

Corresponding author

Correspondence to Phoebe A. Rice.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file contains Supplementary Tables 1-3, Supplementary Figures 1-5 with legends and References. (PDF 1906 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Zhang, A., Pigli, Y. & Rice, P. Structure of the LexA–DNA complex and implications for SOS box measurement. Nature 466, 883–886 (2010). https://doi.org/10.1038/nature09200

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nature09200

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