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Regulation of substrate specificity of p97 by cofactors

Research Project

Project/Area Number 21H02418
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Review Section Basic Section 43020:Structural biochemistry-related
Research InstitutionTottori University

Principal Investigator

Sato Yusuke  鳥取大学, 工学研究科, 准教授 (50568061)

Project Period (FY) 2021-04-01 – 2024-03-31
Project Status Completed (Fiscal Year 2024)
Budget Amount *help
¥17,420,000 (Direct Cost: ¥13,400,000、Indirect Cost: ¥4,020,000)
Fiscal Year 2023: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2022: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2021: ¥8,320,000 (Direct Cost: ¥6,400,000、Indirect Cost: ¥1,920,000)
Keywordsユビキチン / タンパク質分解 / タンパク質複合体 / クライオ電子顕微鏡 / ATPase / 構造予測 / AlphaFold / ユビキチン鎖
Outline of Research at the Start

p97は補因子と共にはたらき、主にユビキチン鎖修飾を受けた基質をアンフォールディングすることでプロテアソーム分解へと導き、多様な細胞機能を制御する。p97が多様な役割を持つのは、ユビキチン鎖修飾の様式が多様である事に加え、p97が約30種類の補因子依存的に基質特異性を獲得しているためである。しかし、ほとんどの補因子についてはp97の基質特異性の決定機構は不明である。本研究では多様な補因子によるp97制御機構を解明するため、生化学的な実験とクライオ電子顕微鏡単粒子解析により、多様な補因子によるp97の基質特異性制御機構を明らかにする。

Outline of Final Research Achievements

Proteins that require degradation in the cell are marked with a molecular tag called a “ubiquitin chain”. Proteins modified by ubiquitin chains are first unfolded by enzymes called p97, and then degraded by a proteolytic enzyme complex known as the proteasome. In this study, we identified three adaptors, FAF1, FAF2, and UBXD7, that enhance the activity of p97. Although the structures of these cofactors could not be observed by cryo-electron microscopy, AI-based structure prediction and biochemical experiments revealed part of the mechanism by which these adaptors enhance p97 activity. The results of this study are scheduled to be submitted for publication within fiscal year 2025.

Academic Significance and Societal Importance of the Research Achievements

細胞が健康を保つためには、不要なタンパク質を適切なタイミングで分解することが大切で、これがうまくいかないとアルツハイマー病やがんなどの様々な病気の原因となる。そのため、タンパク質分解がどのようにコントロールされているかを調べることは、病気の原因や新しい治療法を考えるうえで重要である。本研究では、タンパク質分解の最初の過程で、タンパク質をほどく役割をもつp97という分子に注目し、AIを使った構造予測や実験を通じて、p97の働きを助ける分子がどのように作用するかを明らかにした。この成果は、細胞の中でタンパク質分解がどう制御されているかの理解や、関連する病気の原因解明に役立つと考えられる。

Report

(4 results)
  • 2024 Final Research Report ( PDF )
  • 2023 Annual Research Report
  • 2022 Annual Research Report
  • 2021 Annual Research Report
  • Research Products

    (21 results)

All 2025 2024 2023 2022 2021

All Journal Article (9 results) (of which Peer Reviewed: 9 results,  Open Access: 5 results) Presentation (12 results) (of which Int'l Joint Research: 2 results,  Invited: 2 results)

  • [Journal Article] Combinatorial ubiquitin code degrades deubiquitylation-protected substrates2025

    • Author(s)
      Morita Mai、Takao Miyu、Tokuhisa Honoka、Chiba Ryotaro、Tomomatsu Shota、Akizuki Yoshino、Tomita Takuya、Endo Akinori、Saeki Yasushi、Sato Yusuke、Ohtake Fumiaki
    • Journal Title

      Nature Communications

      Volume: 16 Issue: 1 Pages: 2496-2496

    • DOI

      10.1038/s41467-025-57873-9

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Chemical Diversification of Enzymatically Assembled Polyubiquitin Chains to Decipher the Ubiquitin Codes Programmed on the Branch Structure2024

    • Author(s)
      Furuhata Takafumi、Choi Bumkyu、Uno Taiki、Shinohara Ryota、Sato Yusuke、Okatsu Kei、Fukai Shuya、Okamoto Akimitsu
    • Journal Title

      Journal of the American Chemical Society

      Volume: Online ahead of print Pages: 28538-28552

    • DOI

      10.1021/jacs.4c11279

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A strategy for orthogonal deubiquitination using a bump-and-hole approach2023

    • Author(s)
      Suzuki Takumi、Utsugi Yuki、Yamanaka Satoshi、Takahashi Hirotaka、Sato Yusuke、Sawasaki Tatsuya、Miyamae Yusaku
    • Journal Title

      RSC Chemical Biology

      Volume: 4 Issue: 11 Pages: 879-883

    • DOI

      10.1039/d3cb00095h

    • Related Report
      2023 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Involvement of heterologous ubiquitination including linear ubiquitination in Alzheimer’s disease and amyotrophic lateral sclerosis2023

    • Author(s)
      Sato Yusuke、Terawaki Seigo、Oikawa Daisuke、Shimizu Kouhei、Okina Yoshinori、Ito Hidefumi、Tokunaga Fuminori
    • Journal Title

      Frontiers in Molecular Biosciences

      Volume: 10 Pages: 1089213-1089213

    • DOI

      10.3389/fmolb.2023.1089213

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural biology of the ubiquitin code2022

    • Author(s)
      佐藤 裕介
    • Journal Title

      生化学

      Volume: 94 Issue: 1 Pages: 67-77

    • DOI

      10.14952/SEIKAGAKU.2022.940067

    • ISSN
      0037-1017
    • Year and Date
      2022-02-25
    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Spinocerebellar ataxia type 17-digenic TBP/STUB1 disease: neuropathologic features of an autopsied patient2022

    • Author(s)
      Saito Rie、Tada Yui、Oikawa Daisuke、Sato Yusuke、Seto Makiko、Satoh Akira、Kume Kodai、Ueki Nozomi、Nakashima Masahiro、Hayashi Shintaro、Toyoshima Yasuko、Tokunaga Fuminori、Kawakami Hideshi、Kakita Akiyoshi
    • Journal Title

      Acta Neuropathologica Communications

      Volume: 10 Issue: 1 Pages: 177-177

    • DOI

      10.1186/s40478-022-01486-6

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Identification and molecular analysis of <i>RNF31</i> Q622H germline polymorphism2022

    • Author(s)
      Nakazawa Seshiru、Mamiya Ryo、Kawabata?Iwakawa Reika、Oikawa Daisuke、Kaira Kyoichi、Tokunaga Fuminori、Nobusawa Sumihito、Sato Yusuke、Sasaki Atsushi、Yajima Toshiki、Shirabe Ken
    • Journal Title

      Oncology Letters

      Volume: 24 Issue: 5 Pages: 394-394

    • DOI

      10.3892/ol.2022.13514

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis for the linkage specificity of ubiquitin-binding domain and deubiquitinase2022

    • Author(s)
      Sato Yusuke
    • Journal Title

      The Journal of Biochemistry

      Volume: 172 Issue: 1 Pages: 1-7

    • DOI

      10.1093/jb/mvac031

    • Related Report
      2022 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for specific recognition of K6-linked polyubiquitin chains by the TAB2 NZF domain2021

    • Author(s)
      Li Yanjun、Okatsu Kei、Fukai Shuya、Sato Yusuke
    • Journal Title

      Biophysical Journal

      Volume: 120 Issue: 16 Pages: 3355-3362

    • DOI

      10.1016/j.bpj.2021.06.037

    • Related Report
      2021 Annual Research Report
    • Peer Reviewed
  • [Presentation] Toward elucidation of the mechanism of enhancement of VCP unfoldase activity by Ubx52024

    • Author(s)
      落合 陸斗
    • Organizer
      第97回日本生化学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Analysis of the VCP activation mechanism by the long helix domain of FAF12024

    • Author(s)
      宮内 駿希
    • Organizer
      第97回日本生化学会大会
    • Related Report
      2023 Annual Research Report
  • [Presentation] FAF1 およびUBXD7 のp97 活性化ドメインの同定2023

    • Author(s)
      佐藤 裕介
    • Organizer
      第23回日本蛋白質科学会年会
    • Related Report
      2023 Annual Research Report
  • [Presentation] Introduction of how to use AlphaFold22023

    • Author(s)
      佐藤裕介
    • Organizer
      2024 International Joint Meeting of the 23rd International Conference on Cytochrome P450 and the 38th Annual Meeting of the Japanese Society for the Study of Xenobiotics
    • Related Report
      2023 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ミトコンドリアにおけるユビキチンコード形成と分解の構造基盤2022

    • Author(s)
      佐藤裕介、尾勝圭、深井周也
    • Organizer
      第63回日本生化学会 中国・四国支部例会
    • Related Report
      2022 Annual Research Report
    • Invited
  • [Presentation] RAD23B UBA2ドメインによるK48結合型ユビキチン鎖特異的認識機構2022

    • Author(s)
      佐藤裕介、金澤豪、瓜島絢、角田海斗、日野智也、永野真吾
    • Organizer
      グリーン・サスティナブル・ケミストリー研究センター創立10周年記念シンポジウム
    • Related Report
      2022 Annual Research Report
  • [Presentation] Structural basis for specific recognition of Lys48-linked polyubiquitin chains by the UBA2 domain of RAD23B2022

    • Author(s)
      Yusuke Sato
    • Organizer
      The International Symposium in Tokyo 2022
    • Related Report
      2022 Annual Research Report
    • Int'l Joint Research
  • [Presentation] RAD23B UBA2ドメインによるK48結合型ユビキチン鎖特異的認識機構2022

    • Author(s)
      佐藤裕介、金澤豪、瓜島絢、角田海斗、日野智也、永野真吾
    • Organizer
      第27回日本病態プロテアーゼ学会学術集会
    • Related Report
      2022 Annual Research Report
  • [Presentation] RAD23AによるK48鎖特異的認識機構の構造基盤2022

    • Author(s)
      佐藤裕介、瓜島絢、角田海斗、日野智也、永野真吾
    • Organizer
      第48回生体分子科学討論会
    • Related Report
      2022 Annual Research Report
  • [Presentation] ユビキチンシグナルの構造生物学 奨励賞受賞記念講演2021

    • Author(s)
      佐藤裕介
    • Organizer
      第94回日本生化学大会
    • Related Report
      2021 Annual Research Report
    • Invited
  • [Presentation] RAD23A UBAドメインによるK48結合型ユビキチン鎖特異的認識機構の構造基盤2021

    • Author(s)
      佐藤裕介、瓜島絢、日野智也、永野真吾
    • Organizer
      第94回日本生化学大会
    • Related Report
      2021 Annual Research Report
  • [Presentation] AD23A-UBA2によるK48鎖特異的認識機構の構造基盤2021

    • Author(s)
      佐藤裕介、瓜島絢、日野智也、永野真吾
    • Organizer
      第15回バイオ関連化学シンポジウム
    • Related Report
      2021 Annual Research Report

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Published: 2021-04-28   Modified: 2026-01-16  

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