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:

Crystal structures of the photosystem II D1 C-terminal processing protease

Nature Structural Biology volume 7, pages 749–753 (2000)Cite this article

Abstract

We report here the first three-dimensional structure of the D1 C-terminal processing protease (D1P), which is encoded by the ctpA gene. This enzyme removes the C-terminal extension of the D1 polypeptide of photosystem II of oxygenic photosynthesis. Proteolytic processing is necessary to allow the light driven assembly of the tetranuclear manganese cluster, which is responsible for photosynthetic water oxidation. The X-ray structure of the Scenedesmus obliquus enzyme has been determined at 1.8 Å resolution using the multiwavelength anomalous dispersion method. The enzyme is monomeric and is composed of three folding domains. The middle domain is topologically homologous to known PDZ motifs and is proposed to be the site at which the substrate C-terminus binds. The remainder of the substrate likely extends across the face of the enzyme, interacting at its scissile bond with the enzyme active site Ser 372 / Lys 397 catalytic dyad, which lies at the center of the protein at the interface of the three domains.

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: Structure of D1 protease.
Figure 2: The D1P active site.
Figure 3: Solvent contact surface representation of D1P in its standard orientation.
Figure 4: The PDZ domain.

Similar content being viewed by others

Accession codes

Accessions

Protein Data Bank

References

  1. Takahashi, M., Shiraishi, T. & Asada, K. FEBS Lett. 240, 6–8 (1988).

    Article  CAS  Google Scholar 

  2. Takahashi, Y., Nakane, H., Kojima, H. & Satoh, K. Plant Cell Physiol. 31, 273–280 (1990).

    CAS  Google Scholar 

  3. Nixon, P.J., Trost, J.T. & Diner, B.A. Biochemistry 31, 10859–10871 (1992).

    Article  CAS  Google Scholar 

  4. Metz, J.G., Pakrasi, H., Arntzen, C.J. & Siebert, M. Prog. Photosynth. Res. Proc. Int. Congr. Photosynth. 7th 4, 679–682 (1987).

    Article  CAS  Google Scholar 

  5. Taylor, M.A., Packer, J.C.L. & Bowyer, J.R. FEBS Lett. 237, 229–233 (1988).

    Article  CAS  Google Scholar 

  6. Trost, J.T., Chisholm, D.A., Jordan, D.B. & Diner, B.A. J. Biol. Chem. 272, 20348–20356 (1997).

    Article  CAS  Google Scholar 

  7. Inagaki, N., Yamamoto, Y., Mori, H. & Satoh, K. Plant Mol. Biol. 30, 39–50 (1996).

    Article  CAS  Google Scholar 

  8. Shestakov, S.V. et al. J. Biol. Chem. 269, 19354–19359 (1994).

    CAS  PubMed  Google Scholar 

  9. Hara, H., Yamamoto, Y., Higashitani, A., Suzuki, H. & Nishimura, Y. J. Bacteriol. 173, 4799–4813 (1991).

    Article  CAS  PubMed Central  Google Scholar 

  10. Silber, K.R., Keiler, K.C. & Sauer, R.T. Proc. Natl. Acad. Sci. USA 89, 295–299 (1992).

    Article  CAS  Google Scholar 

  11. Tomb, J.F. et al. Nature 388, 539–547 (1997).

    Article  CAS  Google Scholar 

  12. Keiler, K.C. & Sauer, R.T. J. Biol. Chem. 270, 28864–28868 (1995).

    Article  CAS  Google Scholar 

  13. Paetzel, M. & Dalbey, R.E. Trends Biochem. Sci. 22, 28–31 (1997).

    Article  CAS  Google Scholar 

  14. Tschantz, W.R., Sung, M., Delgado-Partin, V.M. & Dalbey, R.E. J. Biol. Chem. 268, 27349–27354 (1993).

    CAS  PubMed  Google Scholar 

  15. Paetzel, M., Dalbey, R.E. & Strynadka, N.C.J. Nature 396, 186–190 (1998).

    Article  CAS  Google Scholar 

  16. Peat, T.S. et al. Nature 380, 727–730 (1996).

    Article  CAS  Google Scholar 

  17. Slilaty, S.N. & Little, J.W. Proc. Natl. Acad. Sci. USA 84, 3987–3991 (1987).

    Article  CAS  Google Scholar 

  18. Strynadka, N.C.J. et al. Nature 359, 700–705 (1992).

    Article  CAS  Google Scholar 

  19. Rawlings, N.D. & Barrett, A.J. In Proteolysis in cell functions (eds Hopsu-Havu,V.K., Järvinen, M., Kirschke, H.), 13–21 (IOS Press, Amsterdam; 1997).

    Google Scholar 

  20. Kim, J.L. et al. Cell 87, 343–355 (1996).

    Article  CAS  Google Scholar 

  21. Slilaty, S.N. & Vu, H.K. Protein Eng. 4, 919–922 (1991).

    Article  CAS  Google Scholar 

  22. Ponting, C.P. Protein Sci. 6, 464–468 (1997).

    Article  CAS  PubMed Central  Google Scholar 

  23. Beebe, K.D. et al. Biochemistry 39, 3149–3155 (2000).

    Article  CAS  Google Scholar 

  24. Cabral, J.H.M. et al. Nature 382, 649–652. (1996).

    Article  CAS  Google Scholar 

  25. Doyle, D.A. et al. Cell 85, 1067–1076 (1996).

    Article  CAS  Google Scholar 

  26. Hillier, B.J., Christopherson, K.S., Prehoda, K.E., Bredt, D.S. & Lim, W.A. Science 284, 812–815.

  27. Nixon, J.J., Rögner, M. & Diner, B.A. Plant Cell 3, 383–395 (1991).

    Article  CAS  PubMed Central  Google Scholar 

  28. Morden, C.W. & Golden, S.S. Nature 337, 382–385 (1989).

    Article  CAS  Google Scholar 

  29. Otwinowski, Z & Minor, W. Methods Enzymol. 276, 307–326 (1997).

    Article  CAS  PubMed Central  Google Scholar 

  30. Hendrickson, W.A., Horton, J.R. & LeMaster, D.M. EMBO J. 9, 1665–1672 (1990).

    Article  CAS  PubMed Central  Google Scholar 

  31. Sheldrick, G.M. In Direct methods for solving macromolecular structures (ed. Fortier, S.), 131–141 (Kluwer Academic Publishers, Dordrecht; 1998).

    Book  Google Scholar 

  32. Furey, W. & Swaminathan, S. Methods Enzymol. 277, 590–619 (1997).

    Article  CAS  Google Scholar 

  33. Cowtan, K. Joint CCP4 (1994) and ESF-EACBM Newsletter on Protein Crystallography 31, 34–38 (1994).

    Google Scholar 

  34. Collaborative Computational Project, Number 4. CCP4 Suite: programs for protein crystallography. Acta Crystallogr. D 50, 760–763 (1994).

  35. Jones, T.A., Zou, J.Y., Cowan, S.W. & Kjeldgaard, M. Acta Crystallogr. A 47, 110–119 (1991).

    Article  Google Scholar 

  36. Brünger, A.T., Kuriyan, J. & Karplus, M. Science 235, 458–460 (1987).

    Article  Google Scholar 

  37. Tronrud, D.E. Acta Crystallogr. A 48, 912–916 (1991).

    Article  Google Scholar 

  38. Navaza, J. Acta Crystallogr. A 50, 157–163 (1994).

    Article  Google Scholar 

Download references

Acknowledgements

We thank J. Wang for her contributions to the early stage of this project and M. Nelson for helpful discussions. This paper is Contribution No. 8074 of the Central Research and Development Department of E. I. du Pont de Nemours & Co.

Author information

Authors and Affiliations

  1. E. I. du Pont de Nemours & Company, Central Research and Development, Experimental Station, Wilmington, 19880, Delaware, USA

    Der-Ing Liao, Jin Qian, Dexter A. Chisholm & Bruce A. Diner

  2. DuPont Pharmaceuticals Company, Experimental Station, Wilmington, 19880, Delaware, USA

    Douglas B. Jordan

Authors
  1. Der-Ing Liao
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jin Qian
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dexter A. Chisholm
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Douglas B. Jordan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Bruce A. Diner
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Der-Ing Liao or Bruce A. Diner.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Liao, DI., Qian, J., Chisholm, D. et al. Crystal structures of the photosystem II D1 C-terminal processing protease. Nat Struct Mol Biol 7, 749–753 (2000). https://doi.org/10.1038/78973

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI: https://doi.org/10.1038/78973

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