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Structural studies of a novel mediator regulating homologous recombination

Research Project

Project/Area Number 22370045
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionThe University of Tokyo

Principal Investigator

SHIMIZU Toshiyuki  東京大学, 大学院・薬学系研究科, 教授 (30273858)

Project Period (FY) 2010 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥18,590,000 (Direct Cost: ¥14,300,000、Indirect Cost: ¥4,290,000)
Fiscal Year 2012: ¥5,330,000 (Direct Cost: ¥4,100,000、Indirect Cost: ¥1,230,000)
Fiscal Year 2011: ¥5,590,000 (Direct Cost: ¥4,300,000、Indirect Cost: ¥1,290,000)
Fiscal Year 2010: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000)
Keywords相同組み換え / メディエーター / リコンビナーゼ / X線結晶構造解析 / X線結晶解析
Research Abstract

Rad51 has a central role in recombination, assembling onto single-stranded DNA as a nucleoprotein filament and catalyzing the invasion and exchange of homologous DNA sequences. Generally, Rad51 requires the assistance of mediators to overcome the inhibition by RPA. The Swi5-Sfr1 complex has been identified as a mediator, and recent studies have shown that it can activate recombinases directly, and thus this complex is the first molecule for the recombinase activator.We describe the crystal structure of the C-terminal half of Sfr1 in complex with Swi5 from S. pombe. Swi5 and Sfr1 form a parallel coiled-coil heterodimer, joined firmly together by formation of two newly identified leucine-zipper motifs and a bundle. Remarkably, the coiled-coil is sharply kinked, generating an elongated and curved shape. This molecular shape is suitable for binding within the reconstituted helical groove of the Rad51 filament, causing the activation of Rad51 filament by stabilizing it as an active form with a longer helical pitch. Biochemical analysis shows that the C-terminal region of Sfr1 complexed with Swi5 possesses the essential function of Swi5-Sfr1 for a recombination activator, while the N-terminal region of Sfr1 plays a role for the efficient recruitment of the Swi5-Sfr1 complex. Swi5-Sfr1 is conserved from yeast to humans, and therefore the phenomena presented here would be prevalent among all eukaryotic organisms.

Report

(4 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Annual Research Report
  • 2010 Annual Research Report
  • Research Products

    (29 results)

All 2013 2012 2011 2010 Other

All Journal Article (19 results) (of which Peer Reviewed: 19 results) Presentation (8 results) (of which Invited: 2 results) Book (1 results) Remarks (1 results)

  • [Journal Article] Characterisation of an intrinsically disordered protein complex of Swi5-Sfr1 by ion mobility mass spectrometry and small-angle X-ray scattering2013

    • Author(s)
      Saikusa K, Kuwabara N, Kokabu Y, Inoue Y, Sato M, Iwasaki H, Shimizu T, Ikeguchi M, Akashi S
    • Journal Title

      Analyst

      Volume: 138 Pages: 1441-1449

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mechanistic insights into the activation of Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex2013

    • Author(s)
      N.Kuwabara, Y.Murayama, H.Hashimoto, Y.Kokabu, M.Ikeguchi, M.Sato, K.Mayanagi, Y.Tsutsui, H.Iwasaki,and T.Shimizu
    • Journal Title

      Structure

      Volume: 20 Issue: 3 Pages: 440-449

    • DOI

      10.1016/j.str.2012.01.005

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mechanistic insights into the activation of rad51-mediated strand exchange from the structure of a recombination activator, the swi5-sfr1 complex2012

    • Author(s)
      Kuwabara N, Murayama Y, Hashimoto H, Kokabu Y, Ikeguchi M, Sato M, Mayanagi K, Tsutsui Y, Iwasaki H, Shimizu T
    • Journal Title

      Structure

      Volume: 20 Pages: 440-449

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Structure of Human β-Galactosidase: The Structural Basis of GM1 Gangliosidosis and Morquio B Diseases2012

    • Author(s)
      Ohto U, Usui K, , Ochi T, ,Yuki K, Satow Y andShimizu T
    • Journal Title

      J. Biol. Chem

      Volume: 287 Pages: 1801-1812

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Structure of Human β-Galactosidase: The Structural Basis of GM1 Gangliosidosis and Morquio B Diseases2012

    • Author(s)
      Ohto U, et al.
    • Journal Title

      J.Biol.Chem.

      Volume: 287 Issue: 3 Pages: 1801-1812

    • DOI

      10.1074/jbc.m111.293795

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural analyses of human Toll-like receptor polymorphisms D299G and T399I2012

    • Author(s)
      Ohto U, Yamakawa N, Akashi-Takamura S, Miyake K, Shimizu T
    • Journal Title

      J Biol Chem.

      Volume: 287 Issue: 48 Pages: 40611-40617

    • DOI

      10.1074/jbc.m112.404608

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The fission yeast Swi5-Sfr1 complex, an activator of Rad51 recombinase, forms an extremely elongated Dogleg-shaped structure2011

    • Author(s)
      Kokabu Y, Murayama Y, Kuwabara N, Oroguchi T, Hashimoto H, Tsutsui Y, Nozaki N, Akashi S, Unzai S, Shimizu T, Iwasaki H, Sato M, Ikeguchi M
    • Journal Title

      J Biol Chem

      Volume: 286 Pages: 43569-76

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Structures of Mouse and Human RP105/MD-1 Complexes Reveal Unique Dimer Organization of the Toll-Like Receptor Family2011

    • Author(s)
      Ohto U, Miyake K, Shimizu T
    • Journal Title

      J Mol Biol

      Volume: 413 Pages: 815-825

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Fission yeast Swi5-Sfr1 protein complex, an activator of Rad51 recombinase, forms an extremely elongated dogleg-shaped structure2011

    • Author(s)
      Kokabu Y, Murayama Y, Kuwabara N, Oroguchi T, Hashimoto H, Tsutsui Y, Nozaki N, Akashi S, Unzai S, Shimizu T, Iwasaki H, Sato M, Ikeguchi M
    • Journal Title

      J Biol Chem

      Volume: 286 Issue: 50 Pages: 43569-43576

    • DOI

      10.1074/jbc.m111.303339

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal Structures of Mouse and Human RP105/MD-1 Complexes Reveal Unique Dimer Organization of the Toll-Like Receptor Family2011

    • Author(s)
      Ohto, et al.
    • Journal Title

      J.Mol.Biol.

      Volume: 413 Pages: 815-825

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Purification, crystallization and X-ray diffraction study of extracellular dermal glycoprotein from carrot and the inhibition complex it forms with an endo-beta-glucanase from Aspergillus aculeatus2011

    • Author(s)
      T.Yoshizawa, T.Shimizu, H.Hirano, M.Sato, H.Hashimoto
    • Journal Title

      Acta Cryst.

      Volume: F67 Issue: 7 Pages: 830-832

    • DOI

      10.1107/s1744309111020045

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Expression, Purification and crystallization of Swi5 and the Swi5-Sfr1 complex from fission yeast2010

    • Author(s)
      Kokabu Y, Murayama Y, Kuwabara N, Oroguchi T, Hashimoto H, Tsutsui Y, Nozaki N, Akashi S, Unzai S, Shimizu T, Iwasaki H, Sato M, Ikeguchi M
    • Journal Title

      J Biol Chem

      Volume: 286 Pages: 43569-76

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] The structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications2010

    • Author(s)
      Kuwabara, N., Hashimoto, H., Yamada, N., Unzai, S., Ikeguchi, M., Sato, M., Murayama, Y., Iwasaki, H. and Shimizu, T.
    • Journal Title

      Acta Crystallogr

      Volume: F66 Pages: 1124-1126

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Expression, Purification and crystallization of Swi5 and the Swi5-Sfr1 complex from fission yeast2010

    • Author(s)
      Kuwabara, et al
    • Journal Title

      Acta Crystallogr.

      Volume: F66 Pages: 1124-1126

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The structure of the N-terminal regulatory domain of a plant NADPH oxidase and its functional implications2010

    • Author(s)
      Oda, et al
    • Journal Title

      J.Biol.Chem.

      Volume: 285 Pages: 1435-1445

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of human REV7 in complex with a human REV3 fragment and structural implication of the interaction between DNA polymerase ζ and REV12010

    • Author(s)
      Hara, et al
    • Journal Title

      J.Biol.Chem.

      Volume: 285 Pages: 12299-122307

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure and functional implication of zinc-finger domain of Nanos2010

    • Author(s)
      Hashimoto, et al
    • Journal Title

      EMBO reports

      Volume: 11 Pages: 848-853

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and functional characterization of Vibrio parahaemolyticus thermostable direct hemolysin (TDH)2010

    • Author(s)
      Yanagihara, et al
    • Journal Title

      J.Biol.Chem.

      Volume: 285 Pages: 16267-16274

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article]

    • Author(s)
      Oda, T., Hashimoto, H., Kuwabara, N., Akashi, S., Hayashi, K., Kojima, C., Wong, H.L., Kawasaki, T., Shimamoto, K., Sato, M., and Shimizu, T
    • Journal Title

      J.Biol.Chem

      Volume: 285 Pages: 1435-1445

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Presentation] Program for Young Researcher Symposium inEurope'SGC Oxford2012

    • Author(s)
      Toshiyuki Shimizu
    • Organizer
      Mechanistic insights into the activation of the Rad51-mediated strand exchange from the structure of recombination activator, Swi5-Sfr1 complex
    • Place of Presentation
      Oxford, UK
    • Year and Date
      2012-06-08
    • Related Report
      2012 Final Research Report
  • [Presentation] New frontier of the research in RecAfamily recombinases and their accessory proteins (RecA family 2012)2012

    • Author(s)
      Toshiyuki Shimizu
    • Organizer
      Structural study of recombination activator, Swi5-Sfr1 complex
    • Place of Presentation
      Kyoto Royal Hotel & Spa, Kyoto, Japan
    • Related Report
      2012 Final Research Report
  • [Presentation] Structural study of recombination activator, Swi5-Sfr1 complex2012

    • Author(s)
      Shimizu T
    • Organizer
      New frontier of the research in RecAfamily recombinases and their accessory proteins (RecA family 2012)
    • Place of Presentation
      Kyoto Royal Hotel & Spa, Kyoto, Japan
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] Symposium on Structure and Folding of Disease Related Proteins2011

    • Author(s)
      Toshiyuki Shimizu
    • Organizer
      Mechanistic insights into the activation of the Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 complex
    • Place of Presentation
      Seoul National University, Korea
    • Year and Date
      2011-07-08
    • Related Report
      2012 Final Research Report
  • [Presentation] Mechanistic insights into the activation of the Rad51-mediated strand exchange from the structure of a recombination activator, the Swi5-Sfr1 comple2011

    • Author(s)
      Shimizu T
    • Organizer
      Symposium on Structure and Folding of Disease Related Proteins
    • Place of Presentation
      Seoul National University, Korea(招待講演)
    • Year and Date
      2011-07-08
    • Related Report
      2011 Annual Research Report
  • [Presentation] New frontier of the research in Rad51 recombinase and its accessory proteinsInstitut de Biologie Physico Chimique2011

    • Author(s)
      Toshiyuki Shimizu
    • Organizer
      Crystal structure of recombination activator, Swi5-Sfr1 complex, from fission yeast
    • Place of Presentation
      France
    • Related Report
      2012 Final Research Report
  • [Presentation] 関節リウマチ関連タンパク質PAD4の構造科学的研究2010

    • Author(s)
      清水敏之
    • Organizer
      構造生物社会連携シンポジウム
    • Place of Presentation
      東京大学
    • Year and Date
      2010-11-20
    • Related Report
      2010 Annual Research Report
  • [Presentation] Mechanistic insights into the activation of the Rad51-mediated strand exchange from the structure of recombination activator, Swi5-Sfr1 complex

    • Author(s)
      Shimizu T
    • Organizer
      Program for Young Researcher Symposium in Europe
    • Place of Presentation
      Oxford, UK
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Book] 「入門構造生物学」(「転写)部分を担当)2010

    • Author(s)
      清水敏之
    • Total Pages
      199
    • Publisher
      共立出版
    • Related Report
      2010 Annual Research Report
  • [Remarks]

    • URL

      http://www.f.u-tokyo.ac.jp/~kouzou/

    • Related Report
      2012 Final Research Report

URL: 

Published: 2010-08-23   Modified: 2019-07-29  

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