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 a DNA-bound Ultrabithorax–Extradenticle homeodomain complex

Abstract

During the development of multicellular organisms, gene expression must be tightly regulated, both spatially and temporally. One set of transcription factors that are important in animal development is encoded by the homeotic (Hox) genes, which govern the choice between alternative developmental pathways along the anterior–posterior axis1,2. Hox proteins, such as Drosophila Ultrabithorax, have low DNA-binding specificity by themselves but gain affinity and specificity when they bind together with the homeoprotein Extradenticle (or Pbx1 in mammals)3,4. To understand the structural basis of Hox–Extradenticle pairing, we determine here the crystal structure of an Ultrabithorax–Extradenticle–DNA complex at 2.4 Å resolution, using the minimal polypeptides that form a cooperative heterodimer. The Ultrabithorax and Extradenticle homeodomains bind opposite faces of the DNA, with their DNA-recognition helices almost touching each other. However, most of the cooperative interactions arise from the YPWM amino-acid motif of Ultrabithorax—located amino-terminally to its homeodomain—which forms a reverse turn and inserts into a hydrophobic pocket on the Extradenticle homeodomain surface. Together, these protein–DNA and protein–protein interactions define the general principles by which homeotic proteins interact with Extradenticle (or Pbx1) to affect development along the anterior–posterior axis of animals.

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

Access options

Rent or buy this article

Prices vary by article type

from$1.95

to$39.95

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

Figure 1: DNA and protein sequences.
Figure 2: An overview of the Ubx–Exd–DNA ternary complex.
Figure 3: Exd–Ubx structure and DNA interactions.
Figure 4: Protein–protein interactions.

Similar content being viewed by others

References

  1. Lewis, E. B. Agene complex controlling segmentation in Drosophila. Nature 276, 565–570 (1978).

    Article  ADS  CAS  PubMed  Google Scholar 

  2. McGinnis, W. & Krumlauf, R. Homeobox genes and axial patterning. Cell 68, 283–302 (1992).

    Article  CAS  PubMed  Google Scholar 

  3. Mann, R. S. & Chan, S.-K. Extra specificity from extradenticle : the partnership between HOX and exd/pbx homeodomain proteins. Trends Genet. 12, 258–262 (1996).

    Article  CAS  Google Scholar 

  4. Mann, R. S. The specificity of homeotic gene function. Bioessays 17, 855–863 (1995).

    Article  CAS  Google Scholar 

  5. Gehring, W. J., Affolter, M. & Burglin, T. Homeodomain proteins. Annu. Rev. Biochem. 63, 487–526 (1994).

    Article  CAS  Google Scholar 

  6. Wolberger, C. Homeodomain interactions. Curr. Opin. Struct. Biol. 6, 62–68 (1996).

    Article  CAS  Google Scholar 

  7. Lu, Q. & Kamps, M. Structural determinants of Pbx1 mediating cooperative DNA-binding with pentapeptide-containing HOX proteins. Mol. Cell. Biol. 16, 1632–1640 (1996).

    Article  CAS  PubMed  Google Scholar 

  8. Chan, S.-K. & Mann, R. S. Astructural model for an extradenticle-HOX-DNA complex accounts for the choice of HOX protein in the heterodimer. Proc. Natl Acad. Sci. USA 93, 5223–5228 (1996).

    Article  ADS  CAS  Google Scholar 

  9. Chang, C. P., Brocchieri, L., Shen, W. F., Largman, C. & Clearly, M. L. Pbx modulation of Hox homeodomain amino-terminal arms establishes different DNA-binding specificities across the Hox locus. Mol. Cell. Biol. 16, 1734–1745 (1996).

    Article  CAS  PubMed  Google Scholar 

  10. Li, T., Stark, M. R., Johnson, A. D. & Wolberger, C. Crystal structure of the MATa1/MAT alpha 2 homeodomain heterodimer bound to DNA. Science 270, 262–269 (1995).

    Article  ADS  CAS  Google Scholar 

  11. Chan, S. K., Jaffe, L., Capovilla, M., Botas, J. & Mann, R. S. The DNA binding specificity of Ultrabithorax is modulated by cooperative interactions with extradenticle, another homeoprotein. Cell 78, 603–615 (1994).

    Article  CAS  PubMed  Google Scholar 

  12. Fraenkel, E. & Pabo, C. O. Comparison of X-ray and NMR structures for the Antennapedia homeodomain–DNA complex. Nature Struct. Biol. 5, 692–697 (1998).

    Article  CAS  Google Scholar 

  13. Izpisua-Belmonte, J. C., Falkenstein, H., Dolle, P., Renucci, A. & Duboule, D. Murine genes related to teh Drosophila AbdB homeotic gene are sequentially expressed during development of the posterior part of the body. EMBO J. 10, 2279–2289 (1991).

    Article  CAS  PubMed  Google Scholar 

  14. Johnson, F. B., Parker, E. & Krasnow, M. A. Extradenticle protein is a selective cofactor for the Drosophila homeotics: role of the homeodomain and YPWM amino acid motif in the interaction. Proc. Natl Acad. Sci. USA 92, 739–743 (1995).

    Article  ADS  CAS  Google Scholar 

  15. Chan, S.-K., Pöpperl, H., Krumlauf, R. & Mann, R. S. An extradenticle-induced conformational change in a HOX protein overcomes an inhibitory function of the conserved hexapeptide motif. EMBO J. 15, 2477–2488 (1996).

    Google Scholar 

  16. Rauskolb, C., Smith, K., Peifer, M. & Wieschaus, E. Extradenticle determines segmental identities throughout development. Development 121, 3663–3671 (1995).

    CAS  PubMed  Google Scholar 

  17. Klemm, J. D. & Pabo, C. O. Oct-1 POU domain-DNA interactions: cooperative binding of isolated subdomains and effects of covalent linkage. Genes Dev. 10, 27–36 (1996).

    Article  CAS  PubMed  Google Scholar 

  18. Phelan, M. L. & Featherstone, M. S. Distinct HOX N-terminal arm residues are responsible for specificity of DNA recognition by HOX monomers and HOX-PBX heterodimers. J. Biol. Chem. 272, 8635–8643 (1997).

    Article  CAS  PubMed  Google Scholar 

  19. Aggarwal, A. K., Rodgers, D. W., Drottar, M., Ptashne, M. & Harrison, S. C. Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 899–907 (1988).

    Article  ADS  CAS  PubMed  Google Scholar 

  20. Otwinowski, Z. et al. Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335, 321–329 (1988).

    Article  ADS  CAS  Google Scholar 

  21. Tan, S. & Richmond, T. J. Crystal structure of the yeast MATalpha2/MCM1/DNA ternary complex. Nature 391, 660–666 (1998).

    Article  ADS  CAS  Google Scholar 

  22. Janin, J., Miller, S. & Chotia, C. Surface, subunit interfaces and interior of oligomeric proteins. J. Mol. Biol. 204, 155–164 (1988).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  24. Collaborative Computational Project, N. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

    Article  Google Scholar 

  25. Hirsch, J. A. & Aggarwal, A. K. Structure of the even-skipped homeodomain complexed to AT-rich DNA: new perspectives on homeodomain specificity. EMBO J. 14, 6280–6291 (1995).

    Article  CAS  PubMed  Google Scholar 

  26. Brunger, A. T. XPLOR Version 3.1 Manual(Yale Univ., New Haven, (1993).

    Google Scholar 

  27. 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 

  28. de La Fortelle, E. & Bricogne, G. Maximum-likelihood heavy atom parameter refinement for the mutliple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276, 472–494 (1997).

    Article  CAS  Google Scholar 

  29. Evans, S. V. Setor: hardware lighted three-dimensional solid model representations of macromolecules. J. Mol. Graph. 11, 134–138 (1993).

    Article  CAS  Google Scholar 

  30. Nicholls, A., Sharp, K. A. & Honig, B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281–296 (1991).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We thank the staff at CHESS for help with data collection; C. Escalante for advice on protein purification; L. Shapiro for help with map calculations; and T. Jessell and L. Shapiro for comments on this manuscript. J.M.P. thanks the Possen family for their hospitality during trips to CHESS. This work was supported by NIH grants to A.K.A. and R.S.M. R.S.M. is a Scholar of the Leukemia Society of America.

Author information

Authors and Affiliations

Authors

Rights and permissions

Reprints and permissions

About this article

Cite this article

Passner, J., Ryoo, H., Shen, L. et al. Structure of a DNA-bound Ultrabithorax–Extradenticle homeodomain complex. Nature 397, 714–719 (1999). https://doi.org/10.1038/17833

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/17833

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

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