Structural basis for ubiquitin chain-mediated DNA damage responses

• Project/Area Number: 24247014
• Research Category: Grant-in-Aid for Scientific Research (A)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: Fukai Shuya 東京大学, 放射光連携研究機構, 准教授 (10361792)
• Project Period (FY): 2012-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥44,330,000 (Direct Cost: ¥34,100,000、Indirect Cost: ¥10,230,000); Fiscal Year 2015: ¥9,750,000 (Direct Cost: ¥7,500,000、Indirect Cost: ¥2,250,000); Fiscal Year 2014: ¥10,270,000 (Direct Cost: ¥7,900,000、Indirect Cost: ¥2,370,000); Fiscal Year 2013: ¥10,140,000 (Direct Cost: ¥7,800,000、Indirect Cost: ¥2,340,000); Fiscal Year 2012: ¥14,170,000 (Direct Cost: ¥10,900,000、Indirect Cost: ¥3,270,000)
• Keywords: 分子認識 / DNA修復 / タンパク質複合体 / ユビキチン / Ｘ線結晶構造解析 / 構造生物学 / X線結晶構造解析

Outline of Final Research Achievements

Ubiquitin serves as a signaling molecule for regulation of protein degradation and other important cellular functions. In many cases, two or more ubiquitin molecules are tandemly linked through covalent bonding to function as polyubiquitin chains. In this research project, we determined three-dimensional structures of protein complexes that play important roles in synthesis, degradation and recognition of K63-linked polyubiquitin chains (K63 chains) for DNA double strand break (DSB) responses to elucidate mechanisms for the K63 chain-mediated regulation of the DSB responses at atomic resolution. Furthermore, we revealed the structure-function relationships through structure-guided mutational analyses at the molecular and cellular levels.

Research Products

• [Journal Article] Structural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP20 (2015)
  • Author(s): Toma, A, Takahashi, T. S., Sato, Y., Yamagata, A., Goto-Ito, S., Nakada, S., Fukuto, A., Horikoshi, Y., Tashiro, S., Fukai, S.
  • Journal Title: PLoS One Volume: 10 Issue: 3 Pages: 1-15
  • DOI: 10.1371/journal.pone.0120887
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity (2015)
  • Author(s): Sato, Y., Goto, E., Shibata, Y., Kubota, Y., Yamagata, A., Goto-Ito, S., Kubota, K., Inoue, J., Takekawa, M., Tokunaga, F. and Fukai, S.
  • Journal Title: Nat. Struct. Mol. Biol. Volume: 22 Issue: 3 Pages: 222-229
  • DOI: 10.1038/nsmb.2970
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Core structures of ubiquitin dictate its dynamics and function (2014)
  • Author(s): Fukai, S.
  • Journal Title: Journal of Molecular Biology Volume: 426 Issue: 7 Pages: 1367-1369
  • DOI: 10.1016/j.jmb.2013.12.008
• [Journal Article] Get1 stabilizes an open dimer conformation of get3 ATPase by binding two distinct interfaces. (2012)
  • Author(s): Kubota K, Yamagata A, Sato Y, Goto-Ito S, Fukai S.
  • Journal Title: J Mol Biol. Volume: 422(3) Issue: 3 Pages: 366-75
  • DOI: 10.1016/j.jmb.2012.05.045
  • Peer Reviewed
• [Journal Article] Molecular basis of Lys-63-linked polyubiquitination inhibition by the interaction between human deubiquitinating enzyme OTUB1 and ubiquitin-conjugating enzyme UBC13. (2012)
  • Author(s): Sato Y, Yamagata A, Goto-Ito S, Kubota K, Miyamoto R, Nakada S, Fukai S.
  • Journal Title: J Biol Chem. Volume: 287(31) Issue: 31 Pages: 25860-8
  • DOI: 10.1074/jbc.m112.364752
  • Peer Reviewed
• [Journal Article] ポリユビキチン鎖選択的結合による細胞機能制御 (2012)
  • Author(s): 佐藤裕介，深井周也
  • Journal Title: 生化学 Volume: 84 Pages: 776-779
  • NAID: 10031122383
  • Peer Reviewed
• [Presentation] 化学的なユビキチン鎖合成のための試料調製法の探索 (2015)
  • Author(s): 中村美紅
  • Organizer: BMB2015
  • Place of Presentation: 神戸ポートアイランド（兵庫県・神戸市）
  • Year and Date: 2015-12-02
• [Presentation] ユビキチン鎖による炎症シグナル制御の構造基盤 (2014)
  • Author(s): 深井 周也
  • Organizer: 第87回日本生化学会大会
  • Place of Presentation: 国立京都国際会館
  • Year and Date: 2014-10-15
  • Invited
• [Presentation] 中程度の分解能での結晶構造解析 (2014)
  • Author(s): 深井 周也
  • Organizer: 第14回日本蛋白質科学会年会
  • Place of Presentation: ワークピア横浜
  • Year and Date: 2014-06-27
  • Invited
• [Presentation] Structural basis for selective cleavage of M1- and K63-linked polyubiquitin chains by a CYLD deubiquitinase (2013)
  • Author(s): Shuya Fukai, Yusuke Sato
  • Organizer: Cold Spring Harbor Laboratory 2013 meeting - The Ubiquitin Family
  • Place of Presentation: Cold Spring Harbor Laboratory, 米国
  • Invited
• [Presentation] Structural basis for recognition of ubiquitin by UMI domain of RNF168 (2013)
  • Author(s): Yusuke Sato, Aya Toma, Shuya Fukai
  • Organizer: Cold Spring Harbor Laboratory 2013 meeting - The Ubiquitin Family
  • Place of Presentation: Cold Spring Harbor Laboratory, 米国
• [Book] Advanced Methods in Structural Biology (Springer Protocols Handbooks) (2016)
  • Author(s): Shuya Fukai
  • Total Pages: 290
  • Publisher: Springer