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.

Structural basis for selective activation of ABA receptors

Nature Structural & Molecular Biology volume 17, pages 1109–1113 (2010)Cite this article

Subjects

Abstract

Changing environmental conditions and lessening fresh water supplies have sparked intense interest in understanding and manipulating abscisic acid (ABA) signaling, which controls adaptive responses to drought and other abiotic stressors. We recently discovered a selective ABA agonist, pyrabactin, and used it to discover its primary target PYR1, the founding member of the PYR/PYL family of soluble ABA receptors. To understand pyrabactin's selectivity, we have taken a combined structural, chemical and genetic approach. We show that subtle differences between receptor binding pockets control ligand orientation between productive and nonproductive modes. Nonproductive binding occurs without gate closure and prevents receptor activation. Observations in solution show that these orientations are in rapid equilibrium that can be shifted by mutations to control maximal agonist activity. Our results provide a robust framework for the design of new agonists and reveal a new mechanism for agonist selectivity.

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

Prices vary by article type

from$1.95

to$39.95

Learn more

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

Figure 1: Pyrabactin binds the ABA binding pocket of PYR1 and induces gate closure.
Figure 2: Crystal structure of the PYL2–pyrabactin complex.
Figure 3: Genetic identification of pyrabactin selectivity determinants.
Figure 4: Ligand orientation polymorphisms underlie selectivity.

Accession codes

Primary accessions

Protein Data Bank

Referenced accessions

Protein Data Bank

References

  1. Nambara, E. & Marion-Poll, A. Abscisic acid biosynthesis and catabolism. Annu. Rev. Plant Biol. 56, 165–185 (2005).

    Article  CAS  PubMed  Google Scholar 

  2. Cutler, S., Rodriguez, P.L., Finkelstein, R.R. & Abrams, S.R. Abscisic acid: emergence of a core signaling network. Annu. Rev. Plant Biol. 61, 651–679 (2009).

    Article  Google Scholar 

  3. Wang, Y. et al. Molecular tailoring of farnesylation for plant drought tolerance and yield protection. Plant J. 43, 413–424 (2005).

    Article  CAS  PubMed  Google Scholar 

  4. Rademacher, W., Maisch, R., Liessegang, J. & Jung, J. Water consumption and yield formation in crop plants under the influence of synthetic analogues of abscisic acid. in Plant Growth Regulators for Agricultural and Amenity Use Vol. 36 (eds. Hawkins, A.F., Stead, A.D. & Pinfield, N.J.) 53–66 (British Crop Protection Council Publications, Thornton Heath, London, 1987).

  5. Park, S.Y. et al. Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324, 1068–1071 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  6. Iyer, L.M., Koonin, E.V. & Aravind, L. Adaptations of the helix-grip fold for ligand binding and catalysis in the START domain superfamily. Proteins 43, 134–144 (2001).

    Article  CAS  PubMed  Google Scholar 

  7. Szostkiewicz, I. et al. Closely related receptor complexes differ in their ABA selectivity and sensitivity. Plant J. 61, 25–35 (2010).

    Article  CAS  PubMed  Google Scholar 

  8. Ma, Y. et al. Regulators of PP2C phosphatase activity function as abscisic acid sensors. Science 324, 1064–1068 (2009).

    CAS  PubMed  Google Scholar 

  9. Santiago, J. et al. The abscisic acid receptor PYR1 in complex with abscisic acid. Nature 462, 665–668 (2009).

    Article  CAS  PubMed  Google Scholar 

  10. Nishimura, N. et al. Structural mechanism of abscisic acid binding and signaling by dimeric PYR1. Science 326, 1373–1379 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Miyazono, K. et al. Structural basis of abscisic acid signalling. Nature 462, 609–614 (2009).

    Article  CAS  PubMed  Google Scholar 

  12. Yin, P. et al. Structural insights into the mechanism of abscisic acid signaling by PYL proteins. Nat. Struct. Mol. Biol. 16, 1230–1236 (2009).

    Article  CAS  PubMed  Google Scholar 

  13. Melcher, K. et al. A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors. Nature 462, 602–608 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Volkman, B.F., Lipson, D., Wemmer, D.E. & Kern, D. Two-state allosteric behavior in a single-domain signaling protein. Science 291, 2429–2433 (2001).

    Article  CAS  PubMed  Google Scholar 

  15. Melcher, K. et al. Identification and mechanism of ABA receptor antagonism. Nat. Struct. Mol. Biol. doi:10.1038/nsmb.1887 (published online 22 Aug 2010).

  16. Yuan, X. et al. Single amino acid alteration between valine and isoleucine determines the distinct pyrabactin selectivity by PYL1 and PYL2. J. Biol. Chem. doi:10.1074/jbc.M110.160192 (published online 14 July 2010).

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

    Article  CAS  PubMed  Google Scholar 

  18. Frederick, R.O. et al. Small-scale, semi-automated purification of eukaryotic proteins for structure determination. J. Struct. Funct. Genomics 8, 153–166 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. McCoy, A.J., Grosse-Kunstleve, R.W., Storoni, L.C. & Read, R.J. Likelihood-enhanced fast translation functions. Acta Crystallogr. D Biol. Crystallogr. 61, 458–464 (2005).

    Article  PubMed  Google Scholar 

  20. Storoni, L.C., McCoy, A.J. & Read, R.J. Likelihood-enhanced fast rotation functions. Acta Crystallogr. D Biol. Crystallogr. 60, 432–438 (2004).

    Article  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  22. Painter, J. & Merritt, E.A. Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr. D Biol. Crystallogr. 62, 439–450 (2006).

    Article  PubMed  Google Scholar 

  23. Painter, J. & Merritt, E.A. TLSMD web server for the generation of multi-group TLS models. J. Appl. Crystallogr. 39, 109–111 (2006).

    Article  CAS  Google Scholar 

  24. Collaborative Computational Project, Number 4. The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr 50, 760–763 (1994).

  25. 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  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  Google Scholar 

  27. Moriarty, N.W., Grosse-Kunstleve, R.W. & Adams, P.D. electronic Ligand Builder and Optimization Workbench (eLBOW): a tool for ligand coordinate and restraint generation. Acta Crystallogr. D Biol. Crystallogr. 65, 1074–1080 (2009).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Vidal, M., Brachmann, R.K., Fattaey, A., Harlow, E. & Boeke, J.D. Reverse two-hybrid and one-hybrid systems to detect dissociation of protein-protein and DNA-protein interactions. Proc. Natl. Acad. Sci. USA 93, 10315–10320 (1996).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgements

S.R.C. thanks Jeffrey Bachant (Univ. of California, Riverside) for sharing yeast strains. This work was supported by the US National Institute of General Medical Sciences Protein Structure Initiative (U54 GM074901) and the US National Science Foundation (IOS-003725-002). We acknowledge the Life Sciences Collaborative Access Team at sector 21 at the Advanced Photon Source at Argonne National Laboratory for X-ray beamline access.

Author information

Author notes

  1. Francis C Peterson and E Sethe Burgie: These authors contributed equally to this work.

Authors and Affiliations

  1. Department of Biochemistry and Center for Eukaryotic Structural Genomics, Medical College of Wisconsin, Milwaukee, Wisconsin, USA

    Francis C Peterson, Davin R Jensen, Joshua J Weiner & Brian F Volkman

  2. Department of Biochemistry and Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison, Wisconsin, USA

    E Sethe Burgie, Craig A Bingman & George N Phillips Jr

  3. Department of Botany and Plant Sciences and the Center for Plant Cell Biology, University of California-Riverside, Riverside, California, USA

    Sang-Youl Park & Sean R Cutler

  4. Department of Chemistry, University of California-Riverside, Riverside, California, USA

    Chia-En A Chang & Sean R Cutler

Authors
  1. Francis C Peterson
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. E Sethe Burgie
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Sang-Youl Park
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Davin R Jensen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Joshua J Weiner
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Craig A Bingman
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Chia-En A Chang
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Sean R Cutler
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. George N Phillips Jr
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Brian F Volkman
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

F.C.P., E.S.B. and C.A.B. solved crystal structures; S.-Y.P. performed assays and carried out cloning of ABA receptors and mutagenesis studies; J.J.W. performed NMR analysis; D.R.J. purified proteins and contributed to crystallization screening; C.-A.C. performed modeling studies; G.N.P., S.R.C. and B.F.V. supervised the work, interpreted data and contributed to the writing of the manuscript.

Corresponding authors

Correspondence to Sean R Cutler, George N Phillips Jr or Brian F Volkman.

Ethics declarations

Competing interests

S.R.C. holds a related patent application; the S.R.C. laboratory receives research funding from Syngenta.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–3 and Supplementary Table 1 (PDF 462 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Peterson, F., Burgie, E., Park, SY. et al. Structural basis for selective activation of ABA receptors. Nat Struct Mol Biol 17, 1109–1113 (2010). https://doi.org/10.1038/nsmb.1898

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nsmb.1898

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