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Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes

Nature Structural & Molecular Biology volume 15, pages 228–236 (2008)Cite this article

Abstract

Eukaryotic 20S proteasomes are composed of two α-rings and two β-rings, which form an αββα stacked structure. Here we describe a proteasome-specific chaperone complex, designated Dmp1–Dmp2, in budding yeast. Dmp1–Dmp2 directly bound to the α5 subunit to facilitate α-ring formation. In Δdmp1 cells, α-rings lacking α4 and decreased formation of 20S proteasomes were observed. Dmp1–Dmp2 interacted with proteasome precursors early during proteasome assembly and dissociated from the precursors before the formation of half-proteasomes. Notably, the crystallographic structures of Dmp1 and Dmp2 closely resemble that of PAC3—a mammalian proteasome-assembling chaperone; nonetheless, neither Dmp1 nor Dmp2 showed obvious sequence similarity to PAC3. The structure of the Dmp1–Dmp2–α5 complex reveals how this chaperone functions in proteasome assembly and why it dissociates from proteasome precursors before the β-rings are assembled.

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Figure 1: Identification of Dmp1 and Dmp2.
Figure 2: Characterization of the Dmp1–Dmp2 complex.
Figure 3: Impaired 20S proteasome assembly in Δdmp1 cells.
Figure 4: Detection of abnormal α-rings lacking α4 in Δdmp1 and Δdmp2 cells.
Figure 5: Structure of the Dmp1–Dmp2 complex.
Figure 6: Structure of the Dmp1–Dmp2–α5 complex.
Figure 7: Structural similarity between Dmp1–Dmp2 and the human PAC3.

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Acknowledgements

We thank all of the members of BL44XU, especially E. Yamashita and M. Yoshimura, for their help in data collection at SPring-8 and T. Hikage for his help in X-ray diffraction data collection for PAC3. This work was supported by grants from Japan Science and Technology Agency (to S.M.), the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan (to H.Y., T.M., S.M., E.K., K.K. and K. Tanaka) and the Target Protein Project of MEXT (to T.M., K.K. and K. Tanaka and the Takeda Science Foundation (to K. Tanaka)). E.S. is a recipient of a Japan Society for the Promotion of Science Research Fellowship for Young Scientists.

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Author notes

  1. Hideki Yashiroda and Tsunehiro Mizushima: These authors contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Frontier Science, Core Technology and Research Center, Tokyo Metropolitan Institute of Medical Science, Bunkyo-ku, Tokyo, 113-8613, Japan

    Hideki Yashiroda, Tomie Kameyama, Eri Sakata, Yuko Hirano, Shigeo Murata & Keiji Tanaka

  2. Department of Biotechnology, Graduate School of Engineering, Nagoya University, Chikusa-ku, Nagoya, 464-8603, Japan

    Tsunehiro Mizushima, Kenji Takagi, Atsuo Suzuki & Takashi Yamane

  3. Department of Structural Biology and Biomolecular Engineering, Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya, 467-8603, Japan

    Kenta Okamoto, Eiji Kurimoto, Eri Sakata & Koichi Kato

  4. Link Genomics, Inc., Chuo-ku, Tokyo, 103-0024, Japan

    Hidemi Hayashi & Shin-ichiro Niwa

  5. Proteome Analysis Center, Toho University, Funabashi, Chiba, 274-8510, Japan

    Hidemi Hayashi & Toshihiko Kishimoto

  6. Department of Biomolecular Science, Faculty of Science, Toho University, Funabashi, Chiba, 274-8510, Japan

    Toshihiko Kishimoto

  7. Department of Pathology, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido, 060-8638, Japan

    Masanori Kasahara

  8. Laboratory of Protein Metabolism, Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan

    Shigeo Murata

  9. Institute for Molecular Science, National Institutes of Natural Sciences, 5-1 Higashi-yama, Myodaiji, Okazaki, 444-8787, Japan

    Koichi Kato

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Contributions

H.Y. and T. Kameyama performed all of the yeast experiments. T.M., H.Y., K. Takagi and T.Y. determined the structures of the Dmp1–Dmp2 and Dmp1–Dmp2 Δloop-α5 complexes. K.O., E.K., E.S., A.S., Y.H., S.M., T.Y. and K.K. determined the structure of PAC3. H.H., T. Kishimoto and S.N. conducted the mass spectrometric analysis. M.K. performed phylogenetic analyses. H.Y., T.M., K.K., M.K. and K. Tanaka wrote the paper. All of the authors discussed the results and commented on the manuscript.

Corresponding author

Correspondence to Keiji Tanaka.

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Yashiroda, H., Mizushima, T., Okamoto, K. et al. Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes. Nat Struct Mol Biol 15, 228–236 (2008). https://doi.org/10.1038/nsmb.1386

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