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Structural analysis of the transcription environment factors that engage in crosstalk with metabolic pathways

Planned Research

Project AreaCrosstalk of transcriptional control and energy pathways by hub metabolites
Project/Area Number 23116007
Research Category

Grant-in-Aid for Scientific Research on Innovative Areas (Research in a proposed research area)

Allocation TypeSingle-year Grants
Review Section Biological Sciences
Research InstitutionThe University of Tokyo

Principal Investigator

Shimizu Toshiyuki  東京大学, 薬学研究科(研究院), 教授 (30273858)

Co-Investigator(Renkei-kenkyūsha) TOMA Sachiko  東京大学, 大学院薬学系研究科, 助教 (40363535)
NAKAJIMA Yuka  筑波大学, 生命環境系, 助教 (40399499)
Project Period (FY) 2011-04-01 – 2016-03-31
Project Status Completed (Fiscal Year 2015)
Budget Amount *help
¥92,222,000 (Direct Cost: ¥70,940,000、Indirect Cost: ¥21,282,000)
Fiscal Year 2015: ¥15,691,000 (Direct Cost: ¥12,070,000、Indirect Cost: ¥3,621,000)
Fiscal Year 2014: ¥15,691,000 (Direct Cost: ¥12,070,000、Indirect Cost: ¥3,621,000)
Fiscal Year 2013: ¥19,500,000 (Direct Cost: ¥15,000,000、Indirect Cost: ¥4,500,000)
Fiscal Year 2012: ¥19,370,000 (Direct Cost: ¥14,900,000、Indirect Cost: ¥4,470,000)
Fiscal Year 2011: ¥21,970,000 (Direct Cost: ¥16,900,000、Indirect Cost: ¥5,070,000)
Keywordsアルギニンメチル化 / PRMT / 翻訳後修飾 / SAM / X線結晶構造解析 / アルギニンメチル化酵素 / X線結晶解析 / Roquin / 核内受容体 / X線結晶構造解析 / X線小角散乱 / ビタミンDレセプター / Smad / X線結晶解析 / X線小角散乱 / Mybbpla / Nucleomethylin / p53
Outline of Final Research Achievements

Arginine methylation is a post-translational modification catalyzed by the protein arginine methyltransferase (PRMT) family. PRMT1, the predominant member, is responsible for most of the arginine methylation in the cell, is ubiquitously expressed. In contrast, much less is known about its closely related family member, PRMT8. PRMT7 has a unique domain structure consisting two tandem core domains.
We determine the structures of PRMT8 and PRMT7. PRMT8 forms novel helical assembly in the crystal. The mutant protein disrupting the helical assembly exhibits a different cellular localization and reduced the methyltransferase activity, suggesting that the higher oligomerization state is necessary for the proper function of PRMT8. The N and C-terminal core domain of PRMT7 formed the hetero core-dimer like structure. SAH was observed only in the N-terminal catalytic domain. The obtained structural feature suggests that C-terminal core domain lacks the function of the methyltransferase activity.

Report

(6 results)
  • 2015 Annual Research Report   Final Research Report ( PDF )
  • 2014 Annual Research Report
  • 2013 Annual Research Report
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (22 results)

All 2016 2015 2014 2013 2012 2011 Other

All Journal Article (14 results) (of which Peer Reviewed: 14 results,  Open Access: 3 results,  Acknowledgement Compliant: 3 results) Presentation (6 results) (of which Invited: 1 results) Remarks (2 results)

  • [Journal Article] Novel helical assembly in arginine methyltransferase 82016

    • Author(s)
      Toma-Fukai S, Kim JD, Park KE, Kuwabara N, Shimizu N, Krayukhina E, Uchiyama S, Fukamizu A, Shimizu T
    • Journal Title

      Journal of Molecular Biology

      Volume: 428 Issue: 6 Pages: 1197-1208

    • DOI

      10.1016/j.jmb.2016.02.007

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of human Roquin-2 and its complex with constitutive-decay element RNA.2015

    • Author(s)
      Sakurai, S., Ohto, U., & Shimizu, T.
    • Journal Title

      Acta Crystallogr. Sect. F

      Volume: 71 Issue: 8 Pages: 1048-1054

    • DOI

      10.1107/s2053230x15011887

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Protein arginine methyltransferase 7 has a novel homodimer-like structure formed by tandem repeats2014

    • Author(s)
      Hasegawa, M., Toma-Fukai, S., Kim, JD., Fukamizu, A., and Shimizu, T.
    • Journal Title

      FEBS Letter

      Volume: 588 Issue: 10 Pages: 1942-1948

    • DOI

      10.1016/j.febslet.2014.03.053

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Structural basis of pharmacological chaperoning for human β-galactosidase2014

    • Author(s)
      Suzuki H, et al.
    • Journal Title

      J. Biol. Chem.

      Volume: 289 Issue: 21 Pages: 14560-14568

    • DOI

      10.1074/jbc.m113.529529

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Swi5-Sfr1 protein stimulates Rad51-mediated DNA strand exchange reaction through organization of DNA bases in the presynaptic filament.2014

    • Author(s)
      Fornander LH, Renodon-Corniere A, Kuwabara N, Ito K, Tsutsui Y, Shimizu T, Iwasaki H, Norden B, Takahashi M.
    • Journal Title

      Nucleic Acids Res.

      Volume: 42 Issue: 4 Pages: 2358-2365

    • DOI

      10.1093/nar/gkt1257

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structural basis for vitamin D receptor agonism by novel non-secosteroidal ligands2013

    • Author(s)
      Lisa Asano, Ichiaki Ito, Naoyuki Kuwabara, Tsuyoshi Waku, Junn Yanagisawa, Hiroyuki Miyachi, Toshiyuki Shimizu
    • Journal Title

      FEBS lettters

      Volume: 587 Issue: 7 Pages: 957-963

    • DOI

      10.1016/j.febslet.2013.02.028

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] A nonclassical vitamin D receptor pathway suppresses renal fibrosis2013

    • Author(s)
      Ito I, Waku T, Aoki M, Abe R, Nagai Y, Watanabe T, Nakajima Y, Ohkido I, Yokoyama K, Miyachi H, Shimizu T, Murayama A, Kishimoto H, Nagasawa K, Yanagisawa J.
    • Journal Title

      Journal of Clinical Investigation

      Volume: 123 Issue: 11 Pages: 4579-4594

    • DOI

      10.1172/jci67804

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [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

      Analys

      Volume: 138 Issue: 5 Pages: 1441-14499

    • DOI

      10.1039/c2an35878f

    • NAID

      120006557136

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Peroxisome proliferator-activated receptors (PPARs) have multiple binding points2012

    • Author(s)
      Kuwabara N, Oyama T, Tomioka D, Ohashi M, Yanagisawa J, Shimizu T, Miyachi H.
    • Journal Title

      J. Med.Chem.

      Volume: 55 Issue: 2 Pages: 893-902

    • DOI

      10.1021/jm2014293

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-22012

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

      Proc Natl Acad Sci U S A.

      Volume: 109 Issue: 19 Pages: 7421-7426

    • DOI

      10.1073/pnas.1201193109

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis of recruitment of DNA polymerase z by interaction between REV1 and REV72012

    • Author(s)
      Sotaro Kikuchi
    • Journal Title

      J Biol Chem

      Volume: 287 Issue: 40 Pages: 33847-33852

    • DOI

      10.1074/jbc.m112.396838

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystallization of Bg7S, Purification, crystallization and X-ray diffraction study of basic 7S globulin from soybean2011

    • Author(s)
      T.Yoshizawa, H.Hashimoto, T.Shimizu, M.Yamabe, N.Shichijo, K.Hanada, H.Hirano, M.Sato
    • Journal Title

      Acta Cryst.

      Volume: F67 Issue: 11 Pages: 87-89

    • DOI

      10.1111/j.1742-4658.2011.08111.x

    • Related Report
      2011 Annual 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] Novel dimer organization of the TLR family as revealed by the crystal structures of mouse and human RP105/MD-1 complex2011

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

      J.Mol.Biol.

      Volume: 413 Issue: 4 Pages: 815-825

    • DOI

      10.1016/j.jmb.2011.09.020

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] Bifunctional enzyme PRMT8が担うPRMT,PLD活性発揮機構の構造生物学的解明2016

    • Author(s)
      藤間祥子
    • Organizer
      フォトンファクトリー研究会
    • Place of Presentation
      高エネルギー加速器研究機構(茨城県つくば市)
    • Year and Date
      2016-03-30
    • Related Report
      2015 Annual Research Report
  • [Presentation] mRNA分解に関与するタンパク質Roquin-2とRNA複合体のX線結晶構造解析2015

    • Author(s)
      櫻井駿也
    • Organizer
      日本結晶学会
    • Place of Presentation
      大阪府立大(大阪府堺市)
    • Year and Date
      2015-10-17
    • Related Report
      2015 Annual Research Report
  • [Presentation] 線虫由来タンパク質アルギニンメチル基転移酵素7 の結晶構造解析2014

    • Author(s)
      長谷川森雄 他
    • Organizer
      日本結晶学会年会
    • Place of Presentation
      東京大学
    • Year and Date
      2014-11-01 – 2014-11-03
    • Related Report
      2014 Annual Research Report
  • [Presentation] Structural basis for vitamin D receptor antagonistic mechanism by 1α, 25-dihydroxyvitamin D3-26, 23-lactams (DLAMs)2013

    • Author(s)
      Asano L, Ito I, Waku T, Nagasawa K, Yanagisawa J, Shimizu T
    • Organizer
      ICSG2013-SLS
    • Place of Presentation
      札幌(北海道)
    • Related Report
      2013 Annual Research Report
  • [Presentation] 自然免疫系受容体TLR4とその関連タンパク質の構造生物学的研究2012

    • Author(s)
      Shimizu T
    • Organizer
      第22回WSフォーラム
    • Place of Presentation
      九州大学
    • Year and Date
      2012-11-17
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] 代謝とクロストークする転写環境形成因子の構造科学的な解明2011

    • Author(s)
      清水敏之
    • Organizer
      Wakoつくばフォーラム
    • Place of Presentation
      筑波和光ホール(招待講演)
    • Year and Date
      2011-11-29
    • Related Report
      2011 Annual Research Report
  • [Remarks] 蛋白構造生物学教室

    • URL

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

    • Related Report
      2014 Annual Research Report
  • [Remarks]

    • URL

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

    • Related Report
      2012 Annual Research Report

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Published: 2011-08-01   Modified: 2019-07-29  

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