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Structural basis for gibberellin recognition by its receptor GID1

Nature volume 456, pages 520–523 (2008)Cite this article

Abstract

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.

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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).

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Acknowledgements

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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Author notes

  1. Asako Shimada, Miyako Ueguchi-Tanaka and Toru Nakatsu: These authors contributed equally to this work.

Authors and Affiliations

  1. Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan ,

    Asako Shimada, Miyako Ueguchi-Tanaka, Hiroko Ohmiya & Makoto Matsuoka

  2. Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida Shimoadachi-cho, Sakyo-ku, Kyoto 606-8501, Japan,

    Toru Nakatsu, Youichi Naoe & Hiroaki Kato

  3. RIKEN Harima Institute at SPring-8, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148 Japan ,

    Toru Nakatsu & Hiroaki Kato

  4. Department of Applied Biological Chemistry, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan,

    Masatoshi Nakajima

Authors
  1. Asako Shimada
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Corresponding authors

Correspondence to Hiroaki Kato or Makoto Matsuoka.

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This file contains a Supplementary Discussion, Supplementary Table 1, Supplementary Figures 1-9 and Supplementary References. (PDF 4325 kb)

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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). https://doi.org/10.1038/nature07546

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