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Structural biology study of the ER-associated degradation machinery based on eukaryotic thermophile genomic information

Research Project

Project/Area Number 24770102
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Structural biochemistry
Research InstitutionNagoya City University

Principal Investigator

SATOH Tadashi  名古屋市立大学, 薬学研究科(研究院), 准教授 (80532100)

Project Period (FY) 2012-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2013: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Fiscal Year 2012: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
Keywords好熱性真核生物 / 立体構造解析 / PDI / グルコシダーゼ / 構造生物学 / X線結晶構造解析 / NMR解析
Research Abstract

In this study, we aimed to understand the molecular recognition and operating mechanisms of quality control machineries responsible for the glycoprotein fate determination (folding, transport, and degradation) in the endoplasmic reticulum. Our distinctive approach includes application of the genome information of eukaryotic thermophiles that can grow at high temperature (about 60 degrees Celsius). Using X-ray crystallography, we successfully determined the first crystal structures of protein disulfide isomerase (PDI) catalyzing disulfide bond formation and isomerization, and the catalytic domain of glycoprotein processing enzyme glucosidase II.

Report

(3 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Research-status Report
  • Research Products

    (47 results)

All 2014 2013 2012 Other

All Journal Article (8 results) (of which Peer Reviewed: 8 results) Presentation (39 results) (of which Invited: 2 results)

  • [Journal Article] Structural Basis for Proteasome Formation Controlled by an Assembly Chaperone Nas22014

    • Author(s)
      Satoh T, Saeki Y, Hiromoto T, Wang YH, Uekusa Y, Yagi H, Yoshihara H, Yagi-Utsumi M, Mizushima T, Tanaka K, Kato K
    • Journal Title

      Structure

      Volume: (掲載確定) Issue: 5 Pages: 731-743

    • DOI

      10.1016/j.str.2014.02.014

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] ATPase activity and ATP-dependent conformational change in the co-chaperone HSP70/HSP90-organizing protein (HOP)2014

    • Author(s)
      S. Yamamoto, GP. Subedi, S. Hanashima, T. Satoh, M. Otaka, H. Wakui, K. Sawada, S. Yokota, Y. Yamaguchi, H. Kubota, H. Itoh
    • Journal Title

      J. Biol. Chem.

      Volume: (in press)

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for disparate sugar-binding specificities in the homologous cargo receptors ERGIC-53 and VIP362014

    • Author(s)
      Tadashi Satoh, Kousuke Suzuki, Takumi Yamaguchi, and Koichi Kato
    • Journal Title

      PLoS ONE

      Volume: 9 Issue: 2 Pages: e87963-e87963

    • DOI

      10.1371/journal.pone.0087963

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] ATPase activity and ATP-dependent conformational change in the co-chaperone HOP.2014

    • Author(s)
      Yamamoto S, Subedi GP, Hanashima S, Satoh T, Otaka M, Wakui H, Sawada KI, Yokota SI, Yamaguchi Y, Kubota H, Itoh H.
    • Journal Title

      Journal of Biological Chemistry

      Volume: 289 Issue: 14 Pages: 9880-9886

    • DOI

      10.1074/jbc.m114.553255

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Recognition of Bisecting N-Acetylglucosamine: Structural basis for asymmetric interaction with the mouse lectin dendritic cell inhibitory receptor 22013

    • Author(s)
      Masamichi Nagae
    • Journal Title

      J. Biol. Chem.

      Volume: 288 Issue: 47 Pages: 33598-33610

    • DOI

      10.1074/jbc.m113.513572

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] An archaeal homolog of proteasome assembly factor functions as a proteasome activator2013

    • Author(s)
      K. Kumoi, T. Satoh, K. Murata, T. Hiromoto, T. Mizushima, Y. Kamiya, M. Noda, S. Uchiyama, H. Yagi, and K. Kato
    • Journal Title

      PLoS ONE

      Volume: 8 Issue: 3 Pages: e60294-e60294

    • DOI

      10.1371/journal.pone.0060294

    • Related Report
      2013 Final Research Report 2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular and structural basis for N-glycan-dependent determination of glycoprotein fates in cells2012

    • Author(s)
      Y.Kamiya, T.Satoh, K.Kato
    • Journal Title

      Biochim.Biophys.Acta-General Subjects

      Volume: (in press) Issue: 9 Pages: 1327-1337

    • DOI

      10.1016/j.bbagen.2011.12.017

    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular and Structural Basis for Sugar Recognition by Mannose 6-Phosphate Receptor Homology Domain-Containing Lectins and Proteins2012

    • Author(s)
      Tadashi Satoh
    • Journal Title

      Trends in Glycoscience and Glycotechnology

      Volume: 24 Issue: 139 Pages: 193-202

    • DOI

      10.4052/tigg.24.193

    • NAID

      10031146671

    • ISSN
      0915-7352, 1883-2113
    • Related Report
      2012 Research-status Report
    • Peer Reviewed
  • [Presentation] 小胞体糖タンパク質フォールディング装置を構成するタンパク質群の構造2014

    • Author(s)
      佐藤匡史,年森隆泰,Tong Zhu,村田和義,山口拓実,矢木真穂,加藤晃一
    • Organizer
      生物学研究日本薬学会134年会
    • Place of Presentation
      熊本
    • Year and Date
      2014-03-28
    • Related Report
      2013 Final Research Report
  • [Presentation] Structural-architecture of the ER glycoprotein folding sensor UDP-glucose : glycoprotein glucosyltransferase (UGGT)2014

    • Author(s)
      T. Zhu, T. Satoh, K. Murata, H. Kamikubo, T. Toshimori, T. Yamaguchi, M. Yagi-Utsumi, and K. Kato
    • Organizer
      2013年度生物物理中部支部会
    • Place of Presentation
      岡崎
    • Year and Date
      2014-03-06
    • Related Report
      2013 Final Research Report
  • [Presentation] 小胞体品質管理に関わるグルコシダーゼIIの基質認識機構の構造基盤2014

    • Author(s)
      年森隆泰,佐藤匡史,Tong Zhu,加藤晃一
    • Organizer
      2013年度生物物理中部支部会
    • Place of Presentation
      岡崎
    • Year and Date
      2014-03-06
    • Related Report
      2013 Final Research Report
  • [Presentation] プロテインジスルフィドイソメラーゼの機能発現におけるミクロ‐マクロ相関の探査2014

    • Author(s)
      稲垣宏弥,植草義徳,神谷由紀子,伊藤暁,奥村久士,佐藤匡史,加藤晃一
    • Organizer
      2013年度生物物理中部支部会
    • Place of Presentation
      岡崎
    • Year and Date
      2014-03-06
    • Related Report
      2013 Final Research Report
  • [Presentation] The structural biology study on ER folding sensor UDP-glucose : glycoprotein glucosyltransferase (UGGT)2013

    • Author(s)
      T. Zhu, K. Murata, T. Toshimori, T. Yamaguchi, M. Yagi-Utsumi, T. Satoh, and K. Kato
    • Organizer
      Yonsei-IMS Seminars on Biomolecular Sciences : Protein Structure and Diseases
    • Place of Presentation
      Busan, Korea
    • Year and Date
      2013-12-16
    • Related Report
      2013 Final Research Report
  • [Presentation] Redox-dependent conformational changes of the substrate-binding region of protein disulfide isomerase2013

    • Author(s)
      K. Inagaki, Y. Uekusa, Y. Kamiya, S. Itoh, H. Okumura, T. Satoh, and K. Kato
    • Organizer
      山田研究会・統合バイオサイエンスシンポジウム
    • Place of Presentation
      伊良湖
    • Year and Date
      2013-11-20
    • Related Report
      2013 Final Research Report
  • [Presentation] Overall structure of ER folding sensor UDP-glucose : glycoprotein glucosyltransferase revealed by EM tomography2013

    • Author(s)
      T. Zhu, K. Murata, T. Toshimori, T. Yamaguchi, M. Yagi-Utsumi, T. Satoh, and K. Kato
    • Organizer
      山田研究会・統合バイオサイエンスシンポジウム
    • Place of Presentation
      伊良湖
    • Year and Date
      2013-11-20
    • Related Report
      2013 Final Research Report
  • [Presentation] EM tomography analysis of ER folding sensor enzyme UDP-glucose : glycoprotein glucosyltransferase2013

    • Author(s)
      T. Zhu, K. Murata, T. Toshimori, T. Yamaguchi, M. Yagi-Utsumi, T. Satoh, and K. Kato
    • Organizer
      平成25年度生理学研究所研究会「電子顕微鏡機能イメージングの医学・生物学への応用」
    • Place of Presentation
      岡崎
    • Year and Date
      2013-11-13
    • Related Report
      2013 Final Research Report
  • [Presentation] Bacterial expression and EM analysis of UDP-glucose glycosyltransferase from a thermophilic fungus2013

    • Author(s)
      T. Zhu, K. Murata, T. Toshimori, M. Yagi-Utsumi, T. Satoh, and K. Kato
    • Organizer
      糖鎖科学中部拠点第11回若手の力フォーラム
    • Place of Presentation
      名古屋
    • Year and Date
      2013-09-09
    • Related Report
      2013 Final Research Report
  • [Presentation] Structural basis underlying the redox-dependent domain rearrangement of the substrate-binding region of protein disulfide isomerase2013

    • Author(s)
      K. Inagaki, Y. Uekusa, Y. Kamiya, T. Satoh, and K. Kato
    • Organizer
      7th International Conference on Structural Genomics (ICSG2013-SLS)
    • Place of Presentation
      札幌
    • Year and Date
      2013-07-30
    • Related Report
      2013 Final Research Report
  • [Presentation] Redox-dependent conformational dynamics of protein disulfide isomerase coupled with exposure of its substrate binding region2012

    • Author(s)
      K. Inagaki, Y. Uekusa, Y. Kamiya, T. Satoh, and K. Kato
    • Organizer
      The 6th International Symposium "Molecular Science of Fluctuations toward Biological Functions
    • Place of Presentation
      京都
    • Year and Date
      2012-12-06
    • Related Report
      2013 Final Research Report
  • [Presentation] Molecular mechanism of redox-dependent domain rearrangement of the substrate-binding region of protein disulfide isomerase2012

    • Author(s)
      K. Inagaki, Y. Uekusa, Y. Kamiya, T. Satoh, and K. Kato
    • Organizer
      第50回生物物理学会年会
    • Place of Presentation
      名古屋
    • Year and Date
      2012-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] Structural insights into proteasome orchestration mechanism through a proteasome assembly factor Nas2

    • Author(s)
      Tadashi Satoh
    • Organizer
      8th Asian Biophysics Association Symposium (ABA Jeju 2013)
    • Place of Presentation
      Jeju, Korea
    • Related Report
      2013 Annual Research Report
  • [Presentation] ERGIC-53/MCFD2 複合体による糖鎖認識の構造基盤

    • Author(s)
      佐藤匡史
    • Organizer
      第59回 日本薬学会東海支部会
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] Mechanistic insights into the proteasome orchestration by a proteasome assembly chaperone Nas2

    • Author(s)
      Tadashi Satoh
    • Organizer
      7th International Conference on Structural Genomics (ICSG2013-SLS)
    • Place of Presentation
      札幌
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural basis underlying the redox-dependent domain rearrangement of the substrate-binding region of protein disulfide isomerase

    • Author(s)
      Koya Inagaki
    • Organizer
      7th International Conference on Structural Genomics (ICSG2013-SLS)
    • Place of Presentation
      札幌
    • Related Report
      2013 Annual Research Report
  • [Presentation] 積荷受容体ERGIC-53/MCFD2による糖鎖認識の構造基盤

    • Author(s)
      佐藤匡史
    • Organizer
      第32回日本糖質学会年会
    • Place of Presentation
      大阪
    • Related Report
      2013 Annual Research Report
  • [Presentation] Bacterial expression and EM analysis of UDP-glucose glycosyltransferase from a thermophilic fungus

    • Author(s)
      Tong Zhu
    • Organizer
      糖鎖科学中部拠点 第11回若手の力フォーラム
    • Place of Presentation
      名古屋
    • Related Report
      2013 Annual Research Report
  • [Presentation] EM tomography analysis of ER folding sensor enzyme UDP-glucose: glycoprotein glucosyltransferase

    • Author(s)
      Tong Zhu
    • Organizer
      平成25年度 生理学研究所研究会「電子顕微鏡機能イメージングの医学・生物学への応用」
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] Interaction mode of a proteasome assembly chaperone Nas2 with the proteasome Rpt5 subunit

    • Author(s)
      Ying-Hui Wang
    • Organizer
      山田研究会・統合バイオサイエンスシンポジウム
    • Place of Presentation
      伊良湖
    • Related Report
      2013 Annual Research Report
  • [Presentation] Overall structure of ER folding sensor UDP-glucose: glycoprotein glucosyltransferase revealed by EM tomography

    • Author(s)
      Tong Zhu
    • Organizer
      山田研究会・統合バイオサイエンスシンポジウム
    • Place of Presentation
      伊良湖
    • Related Report
      2013 Annual Research Report
  • [Presentation] Redox-dependent conformational changes of the substrate-binding region of protein disulfide isomerase

    • Author(s)
      Koya Inagaki
    • Organizer
      山田研究会・統合バイオサイエンスシンポジウム
    • Place of Presentation
      伊良湖
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural basis for proteasome formation mediated by assembly chaperone Nas2

    • Author(s)
      Tadashi Satoh
    • Organizer
      6th Japan-Korea Seminars on Biomolecular Science : Experiments and Simulation
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] An archaeal homolog of proteasome assembly chaperone forms a homotetramer and functions as proteasome activator

    • Author(s)
      Kentaro Kumoi
    • Organizer
      6th Japan-Korea Seminars on Biomolecular Science : Experiments and Simulation
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] NMR characterization of the interaction of a proteasome assembly chaperone Nas2 with the proteasome Rpt5 subunit

    • Author(s)
      Ying-Hui Wang
    • Organizer
      SOKENDAI Asian Winter School "Innovations and Challenges in Molecular Science: From Basics to Cutting-edge Researches”
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural basis for disparate sugar-binding specificities in the homologous cargo receptors ERGIC-53 and VIP36

    • Author(s)
      Tadashi Satoh
    • Organizer
      Yonsei-IMS Seminars on Biomolecular Sciences : Protein Structures and Diseases
    • Place of Presentation
      Busan, Korea
    • Related Report
      2013 Annual Research Report
  • [Presentation] The structural biology study on ER folding sensor UDP-glucose:glycoprotein glucosyltransferase (UGGT)

    • Author(s)
      Tong Zhu
    • Organizer
      Yonsei-IMS Seminars on Biomolecular Sciences : Protein Structures and Diseases
    • Place of Presentation
      Busan, Korea
    • Related Report
      2013 Annual Research Report
  • [Presentation] Structural-architecture of the ER glycoprotein folding sensor UDP-glucose:glycoprotein glucosyltransferase (UGGT)

    • Author(s)
      Tong Zhu
    • Organizer
      2013年度 生物物理中部支部会
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] 小胞体品質管理に関わるグルコシダーゼIIの基質認識機構の構造基盤

    • Author(s)
      年森隆泰
    • Organizer
      2013年度 生物物理中部支部会
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] プロテインジスルフィドイソメラーゼの機能発現におけるミクロ‐マクロ相関の探査

    • Author(s)
      稲垣宏弥
    • Organizer
      2013年度 生物物理中部支部会
    • Place of Presentation
      岡崎
    • Related Report
      2013 Annual Research Report
  • [Presentation] 小胞体糖タンパク質フォールディング装置を構成するタンパク質群の構造生物学研究

    • Author(s)
      佐藤匡史
    • Organizer
      日本薬学会134年会
    • Place of Presentation
      熊本
    • Related Report
      2013 Annual Research Report
  • [Presentation] 古細菌タンパク質PbaBによるATP非依存的プロテアソーム活性化機構の構造基盤

    • Author(s)
      雲井健太郎,佐藤匡史,廣本武史,水島恒裕,神谷由紀子,野田勝紀,内山 進,村田和義,矢木宏和,加藤晃一
    • Organizer
      第76回日本生化学会 中部支部例会・シンポジウム
    • Place of Presentation
      岡崎
    • Related Report
      2012 Research-status Report
  • [Presentation] タンパク質の機能拡張子としての糖鎖を観る

    • Author(s)
      加藤晃一,矢木宏和,神谷由紀子,佐藤匡史
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] 新規プロテアソーム活性化因子PbaB の構造と機能

    • Author(s)
      雲井健太郎,佐藤匡史,矢木宏和,廣本武史,水島恒裕,内山 進,野田勝紀,村田和義,神谷由紀子,加藤晃一
    • Organizer
      第12回日本蛋白質科学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] 糖タンパク質の輸送と分解に関わる細胞内レクチンの構造生物学研究

    • Author(s)
      佐藤匡史
    • Organizer
      第31回 日本糖質学会年会
    • Place of Presentation
      鹿児島
    • Related Report
      2012 Research-status Report
    • Invited
  • [Presentation] Molecular mechanism of redox-dependent domain rearrangement of the substrate-binding region of protein disulfide isomerase

    • Author(s)
      Kouya Inagaki, Yoshinori Uekusa, Yukiko Kamiya, Tadashi Satoh, Koichi Kato
    • Organizer
      第50回 日本生物物理学会年会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] Redox-dependent conformational dynamics of protein disulfide isomerase coupled with exposure of its substrate binding region

    • Author(s)
      Kouya Inagaki, Yoshinori Uekusa, Yukiko Kamiya, Tadashi Satoh, Koichi Kato
    • Organizer
      The 6th International Symposium, Molecular Science of Fluctuations toward Biological Functions
    • Place of Presentation
      京都
    • Related Report
      2012 Research-status Report
  • [Presentation] プロテアソームを構成するサブユニットとその集合因子Ump1pの相互作用解析

    • Author(s)
      大川慶祐,矢木宏和,植草義徳,矢木真穂,水島恒裕,佐藤匡史,佐伯 泰,田中啓二,加藤晃一
    • Organizer
      日本生物物理学会中部支部講演会
    • Place of Presentation
      名古屋
    • Related Report
      2012 Research-status Report
  • [Presentation] プロテアソーム集合因子Nas2を介したプロテアソームの分子集合機構の構造基盤

    • Author(s)
      佐藤匡史,植草義徳,廣本武史,矢木真穂,矢木宏和,水島恒裕,佐伯 泰,田中啓二,加藤晃一
    • Organizer
      日本薬学会 第133回年会
    • Place of Presentation
      横浜
    • Related Report
      2012 Research-status Report

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Published: 2013-05-31   Modified: 2019-07-29  

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