The abscisic acid receptor PYR1 in complex with abscisic acid


The plant hormone abscisic acid (ABA) has a central role in coordinating the adaptive response in situations of decreased water availability as well as the regulation of plant growth and development. Recently, a 14-member family of intracellular ABA receptors, named PYR/PYL/RCAR1,2,3, has been identified. These proteins inhibit in an ABA-dependent manner the activity of a family of key negative regulators of the ABA signalling pathway: the group-A protein phosphatases type 2C (PP2Cs)4,5,6. Here we present the crystal structure of Arabidopsis thaliana PYR1, which consists of a dimer in which one of the subunits is bound to ABA. In the ligand-bound subunit, the loops surrounding the entry to the binding cavity fold over the ABA molecule, enclosing it inside, whereas in the empty subunit they form a channel leaving an open access to the cavity, indicating that conformational changes in these loops have a critical role in the stabilization of the hormone–receptor complex. By providing structural details on the ABA-binding pocket, this work paves the way for the development of new small molecules able to activate the plant stress response.

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Figure 1: The structure of the PYR1 dimer.
Figure 2: Abscisic acid binding.
Figure 3: Conformational changes in the loops surrounding the ABA binding cavity.

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Protein Data Bank

Data deposits

Atomic coordinates and structure factors for the reported crystal structure have been deposited in the Protein Data Bank under accession code 3K90.


  1. 1

    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  ADS  PubMed  PubMed Central  Google Scholar 

  2. 2

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

    CAS  ADS  PubMed  PubMed Central  Google Scholar 

  3. 3

    Santiago, J. et al. Modulation of drought resistance by the abscisic acid-receptor PYL5 through inhibition of clade A PP2Cs. Plant J. 10.1111/j.1365-313X.2009.03981.x (16 July 2009)

  4. 4

    Leung, J. et al. Arabidopsis ABA response gene ABI1: features of a calcium-modulated protein phosphatase. Science 264, 1448–1452 (1994)

    CAS  ADS  Article  Google Scholar 

  5. 5

    Meyer, K., Leube, M. P. & Grill, E. A protein phosphatase 2C involved in ABA signal transduction in Arabidopsis thaliana . Science 264, 1452–1455 (1994)

    CAS  ADS  Article  Google Scholar 

  6. 6

    Rubio, S. et al. Triple loss of function of protein phosphatases type 2C leads to partial constitutive response to endogenous abscisic acid. Plant Physiol. 150, 1345–1355 (2009)

    CAS  Article  Google Scholar 

  7. 7

    Verslues, P. E., Agarwal, M., Katiyar-Agarwal, S., Zhu, J. & Zhu, J. K. Methods and concepts in quantifying resistance to drought, salt and freezing, abiotic stresses that affect plant water status. Plant J. 45, 523–539 (2006)

    CAS  Article  Google Scholar 

  8. 8

    Pandey, S., Nelson, D. C. & Assmann, S. M. Two novel GPCR-type G proteins are abscisic acid receptors in Arabidopsis . Cell 136, 136–148 (2009)

    CAS  Article  Google Scholar 

  9. 9

    Christmann, A. & Grill, E. Are GTGs ABA’s biggest fans? Cell 136, 21–23 (2009)

    CAS  Article  Google Scholar 

  10. 10

    Radauer, C., Lackner, P. & Breiteneder, H. The Bet v 1 fold: an ancient, versatile scaffold for binding of large, hydrophobic ligands. BMC Evol. Biol. 8, 286 (2008)

    Article  Google Scholar 

  11. 11

    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)

    CAS  Article  Google Scholar 

  12. 12

    Gerard, F. C. et al. Unphosphorylated rhabdoviridae phosphoproteins form elongated dimers in solution. Biochemistry 46, 10328–10338 (2007)

    CAS  Article  Google Scholar 

  13. 13

    Ponting, C. P. & Aravind, L. START: a lipid-binding domain in StAR, HD-ZIP and signalling proteins. Trends Biochem. Sci. 24, 130–132 (1999)

    CAS  Article  Google Scholar 

  14. 14

    Ueda, H. & Tanaka, J. The crystal and molecular structure of dl-2-cis-4-trans-abscisic acid. Bull. Chem. Soc. Jpn 50, 1506–1509 (1997)

    Article  Google Scholar 

  15. 15

    Milborrow, B. V. The chemistry and physiology of abscisic acid. Annu. Rev. Plant Physiol. 25, 259–307 (1974)

    CAS  Article  Google Scholar 

  16. 16

    Saez, A., Rodrigues, A., Santiago, J., Rubio, S. & Rodriguez, P. L. HAB1–SWI3B interaction reveals a link between abscisic acid signaling and putative SWI/SNF chromatin-remodeling complexes in Arabidopsis . Plant Cell 20, 2972–2988 (2008)

    CAS  Article  Google Scholar 

  17. 17

    Kabsch, W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26, 795–800 (1993)

    CAS  Article  Google Scholar 

  18. 18

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

    Article  Google Scholar 

  19. 19

    Murshudov, G. N., Vagin, A. A. & Dodson, E. J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D 53, 240–255 (1997)

    CAS  Article  Google Scholar 

  20. 20

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

    CAS  Article  Google Scholar 

  21. 21

    Konarev, P. V., Volkov, V. V., Sololova, A. V., Koch, M. H. J. & Svergun, D. I. PRIMUS: a Windows PC-based system for small-angle scattering data analysis. J. Appl. Crystallogr. 36, 1277–1282 (2003)

    CAS  Article  Google Scholar 

  22. 22

    Svergun, D., Barberato, C. & Koch, M. H. J. CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates. J. Appl. Crystallogr. 28, 768–773 (1995)

    CAS  Article  Google Scholar 

  23. 23

    Wallace, A. C., Laskowski, R. A. & Thornton, J. M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127–134 (1995)

    CAS  Article  Google Scholar 

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We thank A. McArthy and S. Brockhauser for support during X-ray data collection and R. Serrano and S. Cusack for critical reading of the manuscript. We are grateful to the European Synchrotron radiation facility (ESRF) and the EMBL for access to the macromolecular crystallography and BioSAXS beamlines. This work was supported by grant BIO2008-00221 from Ministerio de Educación y Ciencia and Fondo Europeo de Desarrollo Regional and Consejo Superior de Investigaciones Científicas (fellowships to J.S. and R.A.). Access to the high throughput crystallization facility of the Partnership for Structural Biology in Grenoble (PSB) ( was supported by the European Community–Research Infrastructure Action PCUBE under the FP7 ‘Capacities’ specific programme.

Author Contributions J.S. contributed with the cloning, protein purification, ITC, MALLS and helped with crystallization and SAXS experiments. F.D. performed protein purification, crystallization and crystal refinement experiments and helped with X-ray data collection. A.R. supervised SAXS data collection and performed data analysis. M.J. carried out MALLS experiments and analysis. R.A. carried out cloning and protein purification. S.-Y.P. and S.R.C. carried out cloning of mutant PYR1 proteins and contributed to discussions. P.L.R. contributed to discussions and writing of the manuscript. J.A.M. supervised the work and performed data collection, structure solution and refinement as well as writing of the manuscript.

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Correspondence to José Antonio Márquez.

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This file contains Supplementary Tables 1-2, Supplementary Notes and Data, Supplementary References and Supplementary Figures S1-S3 with Legends. (PDF 3650 kb)

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

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