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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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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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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