Structural determinants for pyrabactin recognition in ABA receptors in Oryza sativa

  • Seungsu Han
  • Yeongmok Lee
  • Eun Joo Park
  • Myung Ki Min
  • Yongsang Lee
  • Tae-Houn Kim
  • Beom-Gi Kim
  • Sangho LeeEmail author


Key message

We determined the structure of OsPYL/RCAR3:OsPP2C50 complex with pyrabactin. Our results suggest that a less-conserved phenylalanine of OsPYL/RCAR subfamily I is one of considerations of ABA agonist development for Oryza sativa.


Pyrabactin is a synthetic chemical mimicking abscisic acid (ABA), a naturally occurring phytohormone orchestrating abiotic stress responses. ABA and pyrabactin share the same pocket in the ABA receptors but pyrabactin modulates ABA signaling differently, exhibiting both agonistic and antagonistic effects. To explore structural determinants of differential functionality of pyrabactin, we determined the crystal structure of OsPYL/RCAR3:pyrabactin:OsPP2C50, the first rice ABA receptor:co-receptor complex structure with a synthetic ABA mimicry. The water-mediated interaction between the wedging Trp-259 of OsPP2C50 and pyrabactin is lost, undermining the structural integrity of the ABA receptor:co-receptor. The loss of the interaction of the wedging tryptophan of OsPP2C with pyrabactin appears to contribute to the weaker functionality of pyrabactin. Pyrabactin in the OsPYL/RCAR3:OsPP2C50 complex adopts a conformation different from that in ABA receptors from Arabidopsis. Phe125, specific to the subfamily I of OsPYL/RCARs in the ABA binding pocket, appears to be the culprit for the differential conformation of pyrabactin. Although the gate closure essential for the integrity of ABA receptor:co-receptor is preserved in the presence of pyrabactin, Phe125 apparently restricts accessibility of pyrabactin, leading to decreased affinity for OsPYL/RCAR3 evidenced by phosphatase assay. However, Phe125 does not affect conformation and accessibility of ABA. Yeast two-hybrid, germination and gene transcription analyses in rice also support that pyrabactin imposes a weak effect on the control of ABA signaling. Taken together, our results suggest that phenylalanine substitution of OsPYL/RCARs subfamily I may be one of considerations for ABA synthetic agonist development.


ABA Pyrabactin ABA receptor Type 2C protein phosphatase Oryza sativa 



We thank the staff members at beamline 5C, Pohang Accelerator Laboratory for technical assistance in crystallographic data collection. This work was supported by the Next-Generation BioGreen 21 Program (PJ01335001 and PJ01367602) through the Rural Development Agency and the National Research Foundation of Korea grants awarded by the Basic Science Research Program (NRF-2018R1A2B6004367) and the Science Research Center Program (SRC-2017R1A5A1014560).

Author’s contributions

SL conceived research plans and supervised experiments. SH and SL designed experiments. SH and YL performed most of the experiments and analyzed the data. EJP, MKM, YL, T-HK, and B-GK performed some experiments and analyzed the data for supporting main idea. SH, YL, and SL wrote the article with contributions of all the authors.

Supplementary material

11103_2019_862_MOESM1_ESM.docx (2 mb)
Supplementary material 1 (DOCX 2024 kb)


  1. Adams PD et al (2010) PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D 66:213–221. CrossRefGoogle Scholar
  2. Belin C et al (2006) Identification of features regulating OST1 kinase activity and OST1 function in guard cells. Plant Physiol 141:1316–1327. CrossRefGoogle Scholar
  3. Cao M et al (2013) An ABA-mimicking ligand that reduces water loss and promotes drought resistance in plants. Cell Res 23:1043–1054. CrossRefGoogle Scholar
  4. Cao MJ et al (2017) Combining chemical and genetic approaches to increase drought resistance in plants. Nat Commun 8:1183. CrossRefGoogle Scholar
  5. Cheng Z, Jin R, Cao M, Liu X, Chan Z (2016) Exogenous application of ABA mimic 1 (AM1) improves cold stress tolerance in bermudagrass (Cynodon dactylon). Plant Cell Tissue Organ Cult (PCTOC) 125:231–240. CrossRefGoogle Scholar
  6. Cutler SR, Rodriguez PL, Finkelstein RR, Abrams SR (2010) Abscisic acid: emergence of a core signaling network. Annu Rev Plant Biol 61:651–679. CrossRefGoogle Scholar
  7. Dupeux F et al (2011a) Modulation of abscisic acid signaling in vivo by an engineered receptor-insensitive protein phosphatase type 2C allele. Plant Physiol 156:106–116. CrossRefGoogle Scholar
  8. Dupeux F et al (2011b) A thermodynamic switch modulates abscisic acid receptor sensitivity. EMBO J 30:4171–4184. CrossRefGoogle Scholar
  9. Emsley P, Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132. CrossRefGoogle Scholar
  10. Finkelstein R (2013) Abscisic acid synthesis and response. Arabidopsis Book 11:e0166. CrossRefGoogle Scholar
  11. Fujii H et al (2009) vitro reconstitution of an abscisic acid signalling pathway. Nature 462:660–664. CrossRefGoogle Scholar
  12. González-Guzmán M et al (2014) Tomato PYR/PYL/RCAR abscisic acid receptors show high expression in root, differential sensitivity to the abscisic acid agonist quinabactin, and the capability to enhance plant drought resistance. J Exp Bot 65:4451–4464. CrossRefGoogle Scholar
  13. Han S et al (2017) Modulation of ABA signaling by altering VxGPhiL motif of PP2Cs in Oryza sativa. Mol Plant 10:1190–1205. CrossRefGoogle Scholar
  14. Hauser F, Waadt R, Schroeder JI (2011) Evolution of abscisic acid synthesis and signaling mechanisms. Curr Biol CB 21:R346–R355. CrossRefGoogle Scholar
  15. He Y, Hao Q, Li W, Yan C, Yan N, Yin P (2014) Identification and characterization of ABA receptors in Oryza sativa. PLOS ONE 9:e95246. CrossRefGoogle Scholar
  16. Kim H et al (2012) A rice orthologue of the ABA receptor, OsPYL/RCAR5, is a positive regulator of the ABA signal transduction pathway in seed germination and early seedling growth. J Exp Bot 63:1013–1024. CrossRefGoogle Scholar
  17. Laskowski RA, Swindells MB (2011) LigPlot+: multiple ligand–protein interaction diagrams for drug discovery. J Chem Inf Model 51:2778–2786. CrossRefGoogle Scholar
  18. Li W et al (2013) Molecular basis for the selective and ABA-independent inhibition of PP2CA by PYL13. Cell Res 23:1369–1379. CrossRefGoogle Scholar
  19. Melcher K et al (2009) A gate-latch-lock mechanism for hormone signalling by abscisic acid receptors. Nature 462:602–608. CrossRefGoogle Scholar
  20. Melcher K et al (2010) Identification and mechanism of ABA receptor antagonism. Nat Struct Mol Biol 17:1102–1108. CrossRefGoogle Scholar
  21. Miyakawa T, Fujita Y, Yamaguchi-Shinozaki K, Tanokura M (2013) Structure and function of abscisic acid receptors. Trends Plant Sci 18:259–266. CrossRefGoogle Scholar
  22. Naeem MS, Dai L, Ahmad F, Ahmad A, Li J, Zhang C (2016) AM1 is a potential ABA substitute for drought tolerance as revealed by physiological and ultra-structural responses of oilseed rape. Acta Physiol Plant 38:183. CrossRefGoogle Scholar
  23. Okamoto M et al (2013) Activation of dimeric ABA receptors elicits guard cell closure, ABA-regulated gene expression, and drought tolerance. Proc Natl Acad Sci USA 110:12132–12137. CrossRefGoogle Scholar
  24. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Macromol Crystallogr Pt A 276:307–326. CrossRefGoogle Scholar
  25. Park SY et al (2009) Abscisic acid inhibits type 2C protein phosphatases via the PYR/PYL family of START proteins. Science 324:1068–1071. Google Scholar
  26. Peterson FC et al (2010) Structural basis for selective activation of ABA receptors. Nat Struct Mol Biol 17:1109–1113. CrossRefGoogle Scholar
  27. Schneider CA, Rasband WS, Eliceiri KW (2012) NIH image to ImageJ: 25 years of image analysis. Nat Methods 9:671–675CrossRefGoogle Scholar
  28. Soon FF et al (2012) Molecular mimicry regulates ABA signaling by SnRK2 kinases and PP2C phosphatases. Science 335:85–88. CrossRefGoogle Scholar
  29. Tischer SV, Wunschel C, Papacek M, Kleigrewe K, Hofmann T, Christmann A, Grill E (2017) Combinatorial interaction network of abscisic acid receptors and coreceptors from Arabidopsis thaliana. Proc Natl Acad Sci USA 114:10280–10285. CrossRefGoogle Scholar
  30. Vaidya AS et al (2017) A rationally designed agonist defines subfamily IIIA abscisic acid receptors as critical targets for manipulating transpiration. ACS Chem Biol 12:2842–2848. CrossRefGoogle Scholar
  31. Weng JK, Ye M, Li B, Noel JP (2016) Co-evolution of hormone metabolism and signaling networks expands plant adaptive plasticity. Cell 166:881–893. CrossRefGoogle Scholar
  32. Xiong J-L, Dai L-L, Ma N, Zhang C-L (2018) Transcriptome and physiological analyses reveal that AM1 as an ABA-mimicking ligand improves drought resistance in Brassica napus. Plant Growth Regul. Google Scholar
  33. Yuan X, Yin P, Hao Q, Yan C, Wang J, Yan N (2010) Single amino acid alteration between valine and isoleucine determines the distinct pyrabactin selectivity by PYL1 and PYL2. J Biol Chem 285:28953–28958. CrossRefGoogle Scholar
  34. Zhang X et al (2012) Complex structures of the abscisic acid receptor PYL3/RCAR13 reveal a unique regulatory mechanism. Structure 20:780–790. CrossRefGoogle Scholar
  35. Zhang XL, Jiang L, Xin Q, Liu Y, Tan JX, Chen ZZ (2015) Structural basis and functions of abscisic acid receptors PYLs. Front Plant Sci 6:88. Google Scholar
  36. Zhao Y, Chow TF, Puckrin RS, Alfred SE, Korir AK, Larive CK, Cutler SR (2007) Chemical genetic interrogation of natural variation uncovers a molecule that is glycoactivated. Nat Chem Biol 3:716–721. CrossRefGoogle Scholar

Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  1. 1.Department of Biological SciencesSungkyunkwan UniversitySuwonRepublic of Korea
  2. 2.Department of BiotechnologyDuksung Women’s UniversitySeoulRepublic of Korea
  3. 3.Gene Engineering Division, Department of Agricultural BiotechnologyNational Institute of Agricultural Sciences, Rural Development AdministrationJeonjuRepublic of Korea

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