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Structural basis for gibberellin recognition by its receptor GID1


Gibberellins (GAs) are phytohormones essential for many developmental processes in plants1. A nuclear GA receptor, GIBBERELLIN INSENSITIVE DWARF1 (GID1), has a primary structure similar to that of the hormone-sensitive lipases (HSLs)2,3. Here we analyse the crystal structure of Oryza sativa GID1 (OsGID1) bound with GA4 and GA3 at 1.9 Å resolution. The overall structure of both complexes shows an α/β-hydrolase fold similar to that of HSLs except for an amino-terminal lid. The GA-binding pocket corresponds to the substrate-binding site of HSLs. On the basis of the OsGID1 structure, we mutagenized important residues for GA binding and examined their binding activities. Almost all of them showed very little or no activity, confirming that the residues revealed by structural analysis are important for GA binding. The replacement of Ile 133 with Leu or Val—residues corresponding to those of the lycophyte Selaginella moellendorffii GID1s—caused an increase in the binding affinity for GA34, a 2β-hydroxylated GA4. These observations indicate that GID1 originated from HSL and was further modified to have higher affinity and more strict selectivity for bioactive GAs by adapting the amino acids involved in GA binding in the course of plant evolution.

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Figure 1: Crystal structures of rice GID1 complexed with GA 4 and an HSL homologue.
Figure 2: Architecture of the GA-binding site in rice GID1.
Figure 3: GA binding activity of mutagenized rice GID1.

Accession codes

Primary accessions

Protein Data Bank

Data deposits

Crystallographic coordinates have been deposited in the Protein Data Bank under accession numbers 3EBL (GID1–GA4) and 3ED1 (GID1–GA3).


  1. 1

    Olszewski, N., Sun, T. P. & Gubler, F. Gibberellin signaling: biosynthesis, catabolism, and response pathways. Plant Cell 14 (Suppl.). S61–S80 (2002)

    CAS  Article  Google Scholar 

  2. 2

    Ueguchi-Tanaka, M. et al. GIBBERELLIN INSENSITIVE DWARF1 encodes a soluble receptor for gibberellin. Nature 437, 693–698 (2005)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Ueguchi-Tanaka, M. et al. Molecular interactions of a soluble gibberellin receptor, GID1, with a rice DELLA protein, SLR1, and gibberellin. Plant Cell 19, 2140–2155 (2007)

    CAS  Article  Google Scholar 

  4. 4

    Davies, P. J. (ed.) Plant Hormones: Biosynthesis, Signal Transduction, Action! 3rd edn (Kluwer, 2004)

    Google Scholar 

  5. 5

    Ueguchi-Tanaka, M., Nakajima, M., Ashikari, M. & Matsuoka, M. Gibberellin receptor and its role in gibberellin signaling in plants. Annu. Rev. Plant Biol. 58, 183–198 (2007)

    CAS  Article  Google Scholar 

  6. 6

    Itoh, H., Ueguchi-Tanaka, M. & Matsuoka, M. Molecular biology of gibberellins signaling in higher plants. Int. Rev. Cell Mol. Biol. 268, 191–221 (2008)

    CAS  Article  Google Scholar 

  7. 7

    Hirano, K. et al. The GID1-mediated gibberellin perception mechanism is conserved in the Lycophyte Selaginella moellendorffii but not in the Bryophyte Physcomitrella patens . Plant Cell 19, 3058–3079 (2007)

    CAS  Article  Google Scholar 

  8. 8

    Yasumura, Y., Crumpton-Taylor, M., Fuentes, S. & Harberd, N. P. Step-by-step acquisition of the gibberellin-DELLA growth-regulatory mechanism during land–plant evolution. Curr. Biol. 17, 1225–1230 (2007)

    CAS  Article  Google Scholar 

  9. 9

    Yeaman, S. J. Hormone-sensitive lipase—new roles for an old enzyme. Biochem. J. 379, 11–22 (2004)

    CAS  Article  Google Scholar 

  10. 10

    Krissinel, E. & Henrick, K. Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr. D 60, 2256–2268 (2004)

    CAS  Article  Google Scholar 

  11. 11

    Ileperuma, N. R. et al. High-resolution crystal structure of plant carboxylesterase AeCXE1, from Actinidia eriantha, and its complex with a high-affinity inhibitor paraoxon. Biochemistry 46, 1851–1859 (2007)

    CAS  Article  Google Scholar 

  12. 12

    Ollis, D. L. et al. The α/β hydrolase fold. Protein Eng. 5, 197–211 (1992)

    CAS  Article  Google Scholar 

  13. 13

    Holm, C., Davis, R. C., Osterlund, T., Schotz, M. C. & Fredrikson, G. Identification of the active site serine of hormone-sensitive lipase by site-directed mutagenesis. FEBS Lett. 344, 234–238 (1994)

    CAS  Article  Google Scholar 

  14. 14

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

    CAS  Article  Google Scholar 

  15. 15

    Adams, P. D. et al. PHENIX: building new software for automated crystallographic structure determination. Acta Crystallogr. D 58, 1948–1954 (2002)

    Article  Google Scholar 

  16. 16

    Perrakis, A., Morris, R. & Lamzin, V. S. Automated protein model building combined with iterative structure refinement. Nature Struct. Biol. 6, 458–463 (1999)

    CAS  Article  Google Scholar 

  17. 17

    Roussel, A. & Cambillau, C. Silicon Graphics Geometry Partners Directory, Vol. 81 77–78 (Silicon Graphics, Mountain View, 1991)

    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 

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We thank M. Kawamura, M. Hattori, Y. Yamamoto, K. Aya and T. Matsubara for technical assistance; R. L. Ordonio and M. Tanrikulu for editing of this manuscript; and T. Shimizu, RIKEN, and N. Shimizu, JASRI at SPring-8, for assistance with data collection. This project was funded by the Target Protein Research Program (M.M. and H.K.), Scientific Research (M.M., and M.U.-T.), and Special Coordination Funds for Promoting Science and Technology (H.K.) from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and by research fellowships from the Japan Society for the Promotion of Science (A.S.).

Author Contributions M.M. and H.K. conceived and designed the project; A.S. performed construct design, purification, crystallization and structure determinations; Y.N. assisted purification, crystallization and heavy-atom derivative preparation; T.N. solved and refined the structures; M.U.-T. conducted experimental work including cloning, mutation, expression, purification and two-hybrid assays; H.O. assisted purification; M.N. performed binding assays and helped with critical discussions of the work; M.U.-T., H.K. and M.M. wrote the manuscript; and A.S. and T.N. edited the manuscript.

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Correspondence to Hiroaki Kato or Makoto Matsuoka.

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Shimada, A., Ueguchi-Tanaka, M., Nakatsu, T. et al. Structural basis for gibberellin recognition by its receptor GID1. Nature 456, 520–523 (2008).

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