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.

Identification of an amino acid–base contact in the GCN4–DNA complex by bromouracil-mediated photocrosslinking

Nature volume 359, pages 650–652 (1992)Cite this article

Abstract

THE bZIP DNA-binding proteins are characterized by a 50-amino-acid DNA binding and dimerization motif, consisting of a highly basic DNA-binding region ('b') followed by a leucine zipper dimerization region ('ZIP')1. The best characterized bZIP DNA-binding protein is GCN4, a yeast transcriptional activator2–6. GCN4 binds to a 9-base-pair two-fold-symmetric DNA site, 5'−A−4T−3G−2A−1C0T+1C+2A+3T+4−3' (refs 7–10). A detailed model known as the 'induced helical fork' model has been proposed for the structure of the GCN4–DNA complex4. Using a site-specific bromouracil-mediated photocrosslinking method, we show here that the alanine at position 238 of GCN4 contacts, or is close to, the thymine 5-methyl of A·T at position +3 of the DNA site in the GCN4–DNA complex. Our results strongly support the induced helical fork model4. Our site-specific bromouracil-mediated photocrosslinking method requires no prior information regarding the structure of the protein or the structure of the protein–DNA complex and should be generalizable to DNA-binding proteins that interact with the DNA major groove11,12

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

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it

$39.95

Learn more

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

References

  1. Vinson, C., Sigler, P. & McKnight, S. Science 246, 911–916 (1989).

    Article  ADS  CAS  Google Scholar 

  2. Struhl, K. in Transcriptional Regulation (eds Yamamoto, K. & McKnight, S.) (Cold Spring Harbor Laboratory Press, New York, in the press).

  3. Talanian, R., McKnight, C. J. & Kim, P. Science 249, 769–771 (1990).

    Article  ADS  CAS  Google Scholar 

  4. O'Neil, K., Hoess, R. & DeGrado, W. Science 249, 774–778 (1990).

    Article  ADS  CAS  Google Scholar 

  5. O'Shea, E., Klemm, J., Kim, P. & Alber, T. Science 254, 539–544 (1991).

    Article  ADS  CAS  Google Scholar 

  6. Saudek, V. et al. Biochemistry 30, 1310–1317 (1991).

    Article  CAS  Google Scholar 

  7. Hill, D., Hope, I., Macke, J. & Struhl, K. Science 234, 451–457 (1986).

    Article  ADS  CAS  Google Scholar 

  8. Oliphant, A., Brandl, C. & Struhl, K. Molec. cell. Biol. 9, 2944–2949 (1989).

    Article  CAS  Google Scholar 

  9. Mavrothalassitis, G., Beal, G. & Papas, T. DNA Cell Biol. 9, 783–788 (1990).

    Article  CAS  Google Scholar 

  10. Gartenberg, M., Ampe, C., Steitz, T. & Crothers, D. Proc. natn. Acad. Sci. U.S.A. 87, 6034–6038 (1990).

    Article  ADS  CAS  Google Scholar 

  11. Wick, K. & Matthews, K. J. biol. Chem. 266, 6106–6112 (1991).

    CAS  PubMed  Google Scholar 

  12. Allen, T., Wick, K. & Matthews, K. J. biol. Chem. 266, 6113–6119 (1991).

    CAS  PubMed  Google Scholar 

  13. Hutchinson, F. Q. Rev. Biophys. 6, 201–246 (1973).

    Article  CAS  Google Scholar 

  14. Weiss, M. et al. Nature 347, 575–578 (1990).

    Article  ADS  CAS  Google Scholar 

  15. Weiss, M. Biochemistry 29, 8020–8024 (1990).

    Article  CAS  Google Scholar 

  16. Fried, M. & Crothers, D. Nucleic Acids Res. 9, 6505–6525 (1981).

    Article  CAS  Google Scholar 

  17. Garner, M. & Revzin, A. Nucleic Acids Res. 9, 3047–3060 (1981).

    Article  CAS  Google Scholar 

  18. Fisher, E. & Caruthers, M. Nucleic Acids Res. 7, 401–416 (1979).

    Article  CAS  Google Scholar 

  19. Wharton, R. & Ptashne, M. Nature 326, 888–891 (1987).

    Article  ADS  CAS  Google Scholar 

  20. Gunasekera, A., Ebright, Y. & Ebright, R. J. biol. Chem. 267, 14713–14720 (1992).

    CAS  PubMed  Google Scholar 

  21. Pu, W. & Struhl, K. Nucleic Acids Res. 20, 771–775 (1992).

    Article  CAS  Google Scholar 

  22. Goeddel, D., Yansura, D., Winston, C. & Caruthers, M. J. molec. Biol. 123, 661–687 (1978).

    Article  CAS  Google Scholar 

  23. Brennan, C., van Cleve, M. & Gumport, R. J. biol. Chem. 261, 7270–7278 (1986).

    CAS  PubMed  Google Scholar 

  24. Hayakawa, T., Ono, A. & Ueda, T. Nucleic Acids Res. 16, 4761–4776 (1988).

    Article  CAS  Google Scholar 

  25. Fliess, A., Wolfes, H. & Pingould, A. Nucleic Acids Res. 16, 11781–11793 (1988).

    Article  CAS  Google Scholar 

  26. Risse, G., Jooss, K., Neuberg, M., Brüller, H.-J. & Mu'ller, R. EMBO J 8, 3825–3832 (1989).

    Article  CAS  Google Scholar 

  27. Lin, S.-Y. & Riggs, A. Proc. natn. Acad. Sci. U.S.A. 71, 947–951 (1974).

    Article  ADS  CAS  Google Scholar 

  28. Ogata, R. & Gilbert, W. Proc. natn. Acad. Sci. U.S.A. 74, 4973–4976 (1977).

    Article  ADS  CAS  Google Scholar 

  29. Simpson, R. Cell 18, 277–285 (1979).

    Article  CAS  Google Scholar 

  30. Ebright, R., Ebright, Y. & Gunasekera, A. Nucleic Acids Res. 17, 10295–10305 (1989).

    Article  CAS  Google Scholar 

Download references

Author information

Author notes

  1. Richard H. Ebright: To whom correspondence should be addressed

Authors and Affiliations

  1. Department of Chemistry and Waksman Institute, Rutgers University, New Brunswick, New Jersey, 08855, USA

    Erich E. Blatter, Yon W. Ebright & Richard H. Ebright

Authors
  1. Erich E. Blatter
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Yon W. Ebright
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Richard H. Ebright
    View author publications

    You can also search for this author in PubMed Google Scholar

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Blatter, E., Ebright, Y. & Ebright, R. Identification of an amino acid–base contact in the GCN4–DNA complex by bromouracil-mediated photocrosslinking. Nature 359, 650–652 (1992). https://doi.org/10.1038/359650a0

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/359650a0

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