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

Research Project

Project/Area Number 24687012
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypePartial Multi-year Fund
Research Field Structural biochemistry
Research InstitutionThe 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 *help
¥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.

Report

(6 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • Research Products

    (18 results)

All 2017 2016 2015 2014 2013 2012 Other

All Journal Article (11 results) (of which Peer Reviewed: 11 results,  Open Access: 7 results,  Acknowledgement Compliant: 4 results) Presentation (4 results) Book (2 results) Remarks (1 results)

  • [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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystal structure of Sec10, a subunit of the exocyst complex2017

    • 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

    • Related Report
      2016 Annual Research Report
    • 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

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of Slitrk2-PTPδ complex reveals mechanisms for splicing-dependent trans-synaptic adhesion2015

    • 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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Mechanisms of splicing-dependent trans-synaptic adhesion by PTPδ-IL1RAPL1/IL-1RAcP for synaptic differentiation2015

    • 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

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structural basis for ubiquitin recognition by ubiquitin-binding zinc finger of FAAP202015

    • 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

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structures of CYLD USP with Met1- or Lys63-linked diubiquitin reveal mechanisms for dual specificity2015

    • 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

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Switching and emergence of CTL epitopes in HIV-1 infection2014

    • 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

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure of TCR and antigen complexes at an immunodominant CTL epitope in HIV-1 infection2013

    • 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

    • Related Report
      2013 Annual Research Report
    • 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

    • Related Report
      2012 Annual Research Report
    • 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

    • Related Report
      2012 Annual Research Report
    • 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
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural basis for recognition of ubiquitin by UMI domain of RNF1682013

    • Author(s)
      佐藤裕介
    • Organizer
      THE UBIQUITIN FAMILY
    • Place of Presentation
      Cold Spring Harbor Laboratory
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural basis for specific cleavage of Met1- and Lys63-linked polyubiquitin chains by the USP domain of CYLD2013

    • 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
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural Basis for the Posttranslational Membrane insertion by Get32012

    • 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
    • Related Report
      2012 Annual Research Report
  • [Book] Protein Modifications in Pathogenic Dysregulation of Signaling (Inoue, J. and Takekawa, M., eds.)2015

    • Author(s)
      Sato Y, et al.,
    • Publisher
      Springer
    • Related Report
      2015 Annual Research Report
  • [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
    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.iam.u-tokyo.ac.jp/srro/SRROLifeSciDivJp2/Top.html

    • Related Report
      2012 Annual Research Report

URL: 

Published: 2012-04-24   Modified: 2019-07-29  

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