Abstract

Most G-protein-coupled receptors (GPCRs) are stabilized in common in the inactive state by the formation of the sodium ion–centered water cluster with the conserved Asp2.50 inside the seven-transmembrane domain. We determined the crystal structure of the leukotriene B4 (LTB4) receptor BLT1 bound with BIIL260, a chemical bearing a benzamidine moiety. Surprisingly, the amidine group occupies the sodium ion and water locations, interacts with D662.50, and mimics the entire sodium ion–centered water cluster. Thus, BLT1 is fixed in the inactive state, and the transmembrane helices cannot change their conformations to form the active state. Moreover, the benzamidine molecule alone serves as a negative allosteric modulator for BLT1. As the residues involved in the benzamidine binding are widely conserved among GPCRs, the unprecedented inverse-agonist mechanism by the benzamidine moiety could be adapted to other GPCRs. Consequently, the present structure will enable the rational development of inverse agonists specific for each GPCR.

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Acknowledgements

We are grateful to Y. Nakamura, H. Tanabe, H. Ago, K. Ida and our colleagues at the RIKEN Center for Life Science Technologies for technical advice and useful discussions on sample preparation, crystallization, data processing, and structural refinement. The synchrotron radiation experiments were performed at BL32XU of SPring-8, with the approval of the Japan Synchrotron Radiation Research Institute (JASRI) (Proposal No. 2016B2726). Some of the vectors for the TGFα-shedding assay were kindly donated by J. Aoki and A. Inoue, at Tohoku University. This work was supported by the Platform Project for Supporting Drug Discovery and Life Science Research funded by Japan Agency for Medical Research and Development (AMED) (S.Y.), by Takeda Science Foundation (T.S.), by MEXT/JSPS KAKENHI Grant Numbers 23770133 (T.H.), 15KK0320, 16K08596 (T.O.), 26460061 (M.N.), 15H05897, 15H05904, and 15H04708 (T.Y.), and by Grants-in-Aid from the Foundation of Strategic Research Projects in Private Universities from MEXT (S1311011, S1411007) (T.Y.) and (2013-2017) (M.M.). M.M. received support for another GPCR project from Takeda Pharmaceutical Co. BIIL260 and BIIL284 were kindly provided by Boehringer Ingelheim Pharma GmbH & Co. KG.

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Affiliations

  1. RIKEN Structural Biology Laboratory, Tsurumi-ku, Yokohama, Kanagawa, Japan.

    • Tetsuya Hori
    •  & Shigeyuki Yokoyama
  2. RIKEN SPring-8 Center, Sayo, Hyogo, Japan.

    • Tetsuya Hori
    • , Kunio Hirata
    • , Keitaro Yamashita
    • , Yoshiaki Kawano
    • , Masaki Yamamoto
    •  & Masashi Miyano
  3. Department of Biochemistry, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan.

    • Toshiaki Okuno
    •  & Takehiko Yokomizo
  4. Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.

    • Kunio Hirata
  5. Division of Structural and Synthetic Biology, RIKEN Center for Life Science Technologies, Tsurumi-ku, Yokohama, Japan.

    • Masakatsu Hato
  6. Department of Biochemistry and Molecular Biology, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo, Japan.

    • Motonao Nakamura
    •  & Takao Shimizu
  7. Department of Life Science, Faculty of Science, Okayama University of Science, Kita-ku, Okayama, Japan.

    • Motonao Nakamura
  8. Department of Lipid Signaling, National Center for Global Health and Medicine, Shinjuku, Tokyo, Japan.

    • Takao Shimizu
  9. Department of Chemistry and Biological Science, College of Science and Engineering, Aoyama Gakuin University, Chuo-ku, Sagamihara, Kanagawa, Japan.

    • Masashi Miyano

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Contributions

T.H., T.S., T.Y., M.M., and S.Y. designed the research. T.H. performed all experiments from sample preparation to structure determination and functional analyses, except that T.O. performed the expression of BLT1 mutants using HEK293 cells and the signal assays. K.H., K.Y., Y.K., and M.Y. assisted with the data collection at BL32XU of SPring-8. M.H. constructed the in-house crystallization device and assisted with the crystallization experiment. T.O., M.N., T.S., T.Y., M.M., and S.Y. assisted with the LTB4 binding assay. M.M. supervised the expression, purification, and crystallization in the early stage of the project. S.Y. supervised the purification, crystallization, and structure determination and analysis. T.H. and S.Y. wrote the manuscript, and all of the other authors commented on it.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Shigeyuki Yokoyama.

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DOI

https://doi.org/10.1038/nchembio.2547

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