The structural basis for specific synthesis of Met1-linked polyubiquitin chains by LUBAC

• Project/Area Number: 24687012
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Partial Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: Sato Yusuke 東京大学, 分子細胞生物学研究所, 助教 (50568061)
• Project Period (FY): 2012-04-01 – 2017-03-31
• Project Status: Completed (Fiscal Year 2016)
• Budget Amount: ¥27,430,000 (Direct Cost: ¥21,100,000、Indirect Cost: ¥6,330,000); Fiscal Year 2015: ¥6,240,000 (Direct Cost: ¥4,800,000、Indirect Cost: ¥1,440,000); Fiscal Year 2014: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2013: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000); Fiscal Year 2012: ¥9,750,000 (Direct Cost: ¥7,500,000、Indirect Cost: ¥2,250,000)
• Keywords: ユビキチン / 結晶構造解析 / X線結晶構造解析 / NF-κB

Outline of Final Research Achievements

The aim of this study was to determine the crystal structure of the ubiquitin (Ub) ligase complex LUBAC that specifically synthesizes Met1-linked Ub chain. However, the structure of LUBAC in complex with Ub was determined by the group of Katrin Rittinger in 2013, and therefore we had to change our research theme.
On the other hand, we purified several kinds of enzymes for Ub chain synthesis in the process of LUBAC research. With these enzymes, we succeeded in large-scale preparation of Lys6-, Lys29- and Lys33-linked Ub chains which were difficult to be obtained. In addition, we determined the crystal structures of CYLD in complex with Met1-linked diUb, CYLD in complex with Lys63-linked diUb, FAAP20 in complex with Lys63-linked diUb and USP30 in complex with Lys 6-linked diUb.

Research Products

• [Journal Article] Structural basis of the interaction between Topoisomerase IIIβ and the TDRD3 auxiliary factor. (2017)
  • Author(s): Goto-Ito S, Yamagata A, Takahashi TS, Sato Y, Fukai S.
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 42123-42123
  • DOI: 10.1038/srep42123
  • Peer Reviewed / Open Access
• [Journal Article] Crystal structure of Sec10, a subunit of the exocyst complex (2017)
  • Author(s): Chen J, Yamagata A, Kubota K, Sato Y, Goto-Ito S, Fukai S.
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 40909-40909
  • DOI: 10.1038/srep40909
  • Peer Reviewed / Open Access
• [Journal Article] Distinct Roles for the N- and C-terminal Regions of M-Sec in Plasma Membrane Deformation during Tunneling Nanotube Formation. (2016)
  • Author(s): Kimura S, Yamashita M, Yamakami-Kimura M, Sato Y, Yamagata A, Kobashigawa Y, Inagaki F, Amada T, Hase K, Iwanaga T, Ohno H, Fukai S.
  • Journal Title: Scientific Reports Volume: 6 Issue: 1 Pages: 33548-33548
  • DOI: 10.1038/srep33548
  • NAID: 120005855947
  • Peer Reviewed / Open Access
• [Journal Article] Structure of Slitrk2-PTPδ complex reveals mechanisms for splicing-dependent trans-synaptic adhesion (2015)
  • Author(s): Yamagata A., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Yoshida, T., Fukai , S.
  • Journal Title: Scientific Reports Volume: 5 Issue: 1 Pages: 9686-9686
  • DOI: 10.1038/srep09686
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Mechanisms of splicing-dependent trans-synaptic adhesion by PTPδ-IL1RAPL1/IL-1RAcP for synaptic differentiation (2015)
  • Author(s): Yamagata A., Yoshida, T., Sato, Y., Goto-Ito, S., Uemura, T., Maeda, A., Shiroshima, T., Iwasawa-Okamoto, S., Mori, H., Mishina, M., Fukai , S.
  • Journal Title: Nature Communications Volume: 6 Issue: 1 Pages: 6926-6926
  • DOI: 10.1038/ncomms7926
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [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] Switching and emergence of CTL epitopes in HIV-1 infection (2014)
  • Author(s): Han C, Kawana-Tachikawa A, Shimizu A, Zhu D, Nakamura H, Adachi E, Kikuchi T, Koga M, Koibuchi T, Gao GF, Sato Y, Yamagata A, Martin E, Fukai S, Brumme ZL, Iwamoto A
  • Journal Title: Retrovirology Volume: in press
  • Peer Reviewed
• [Journal Article] Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection (2013)
  • Author(s): Shimizu, A., Kawana-Tachikawa. A., Yamagata, A., Han, C., Zhu, D., Sato, Y., Nakamura, H., Koibuchi, T., Carlson, J., Martin, E., Brumme, C.J., Shi, Y., Gao, G.F., Brumme, Z.L., Fukai, S., Iwamoto, A.
  • Journal Title: Scientific Reports Volume: 3 Issue: 1 Pages: 3097-3097
  • DOI: 10.1038/srep03097
  • 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] 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
• [Presentation] CYLDによるLys63鎖およびMet1鎖特異的切断機構の構造的基盤 (2014)
  • Author(s): 佐藤裕介
  • Organizer: 日本薬学会
  • Place of Presentation: 熊本大学
• [Presentation] Structural basis for recognition of ubiquitin by UMI domain of RNF168 (2013)
  • Author(s): 佐藤裕介
  • Organizer: THE UBIQUITIN FAMILY
  • Place of Presentation: Cold Spring Harbor Laboratory
• [Presentation] Structural basis for specific cleavage of Met1- and Lys63-linked polyubiquitin chains by the USP domain of CYLD (2013)
  • Author(s): 佐藤裕介
  • Organizer: International Conference on Structural Genomics 2013
  • Place of Presentation: 京王プラザホテル札幌
• [Presentation] Structural Basis for the Posttranslational Membrane insertion by Get3 (2012)
  • Author(s): 山形敦史、窪田恵子、伊藤桜子、佐藤裕介、深井周也
  • Organizer: 第35回日本分子生物学会年会
  • Place of Presentation: 福岡国際会議場
  • Year and Date: 2012-12-11
• [Book] Protein Modifications in Pathogenic Dysregulation of Signaling (Inoue, J. and Takekawa, M., eds.) (2015)
  • Author(s): Sato Y, et al.,
  • Publisher: Springer
• [Book] 生化学 (2012)
  • Author(s): 佐藤裕介、深井周也
  • Total Pages: 5
  • Publisher: 日本生化学会
• [Remarks]
  • URL: http://www.iam.u-tokyo.ac.jp/srro/SRROLifeSciDivJp2/Top.html