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Structural study on the clamp PCNA-loading mechanism by the clamp loader RFC

Research Project

Project/Area Number 26440023
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Structural biochemistry
Research InstitutionUniversity of Yamanashi

Principal Investigator

OYAMA Takuji  山梨大学, 総合研究部, 准教授 (60423133)

Co-Investigator(Renkei-kenkyūsha) ISHINO Yoshizumi  九州大学, 農学研究院, 教授 (30346837)
SHIRAI Tsuyoshi  長浜バイオ大学, バイオサイエンス学部, 教授 (00262890)
MAYANAGI Kouta  九州大学, 生体防御医学研究所, 助教 (50418571)
Project Period (FY) 2014-04-01 – 2017-03-31
Project Status Completed (Fiscal Year 2016)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2016: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
Fiscal Year 2015: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2014: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
KeywordsDNA複製 / タンパク質DNA複合体 / 結晶構造解析
Outline of Final Research Achievements

To understand the detailed loading mechanism of the clamp PCNA onto DNA by the clamp-loader RFC in an ATP-dependent manner, we aimed (1) preparation of selenomethionine-labeled (SeMet) PCNA, (2) high resolution structure determination of RFC, and (3) crystallization and structure determination of the RFC-PCNA-DNA ternary complex. We determined the crystal structure of SeMet PCNA at 2.5 angstrom resolution. We established a novel preparation method of the highly purified recombinant RFC, but did not succeed in the high-resolution structure determination of the RFC. We performed crystallization screening of the RFC-PCNA-DNA ternary complex in a wide range of conditions, but obtained no crystals during this research project.

Report

(4 results)
  • 2016 Annual Research Report   Final Research Report ( PDF )
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (20 results)

All 2016 2015 2014 Other

All Journal Article (12 results) (of which Peer Reviewed: 12 results,  Open Access: 2 results,  Acknowledgement Compliant: 2 results) Presentation (3 results) Remarks (5 results)

  • [Journal Article] 細胞内の巨大な分子モーター「ダイニン」の構造解析2016

    • Author(s)
      大山拓次、栗栖源嗣、昆隆英
    • Journal Title

      放射光

      Volume: 29 Pages: 82-89

    • NAID

      40020850525

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Atomic structure of an archaeal GAN suggests its dual roles as an exonuclease in DNA repair and a CMG component in DNA replication.2016

    • Author(s)
      Oyama, T., Ishino, S., Shirai, T., Yamagami, T., Nagata, M., Ogino, H., Kusunoki, M., and Ishino, Y.
    • Journal Title

      Nucleic Acids, Res.

      Volume: 44 Issue: 19 Pages: 9509-9517

    • DOI

      10.1093/nar/gkw789

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Integrated molecular mechanism directing nucleosome reorganization by human FACT2015

    • Author(s)
      Tsunaka Y, Fujiwara Y, Oyama T, Hirose S, Morikawa K
    • Journal Title

      Genes Dev

      Volume: 30(6) Issue: 6 Pages: 673-686

    • DOI

      10.1101/gad.274183.115

    • Related Report
      2016 Annual Research Report 2015 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Different structures of the two peroxisome proliferator-activated receptor gamma (PPARγ) ligand-binding domains in homodimeric complex with partial agonist, but not full agonist2015

    • Author(s)
      M. Ohashi, T. Oyama, H. Miyachi
    • Journal Title

      Bioorganic & Medicinal Chemistry Letters

      Volume: - Issue: 13 Pages: 2639-2644

    • DOI

      10.1016/j.bmcl.2015.04.076

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Peroxisome proliferator-activated receptor gamma (PPARgamma) has multiple binding points that accommodate ligands in various conformations: Structurally similar PPARgamma partial agonists bind to PPARgamma LBD in different conformations2015

    • Author(s)
      Ohashi M, Gamo K, Oyama T, Miyachi H
    • Journal Title

      Bioorg Med Chem Lett

      Volume: 25 Issue: 14 Pages: 2758-2762

    • DOI

      10.1016/j.bmcl.2015.05.025

    • Related Report
      2015 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural design and synthesis of arylalkynyl amide-type peroxisome proliferator-activated receptor γ (PPARγ)-selective antagonists based on the helix12-folding inhibition hypothesis.2015

    • Author(s)
      M. Ohashi, K. Gamo, Y. Tanaka, M. Waki, Y. Beniyama, K. Matsuno, J. Wada, M. Tenta, J. Eguchi, M. Makishima, N. Matsuura, T. Oyama, H. Miyachi.
    • Journal Title

      European Journal of Medicinal Chemistry

      Volume: 90 Pages: 53-67

    • DOI

      10.1016/j.ejmech.2014.11.017

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Modification of Chimeric (2S, 3S)-butanediol dehydrogenase based on structural information.2015

    • Author(s)
      Shimegi T, Mochizuki K, Oyama T, Ohtsuki T, Kusunoki M, Ui S
    • Journal Title

      Protein Pept Lett

      Volume: 22 Pages: 226-233

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Crystallization and preliminary X-ray diffraction analysis of domain chimeric L-(2S, 3S)-butanediol dehydrogenase2014

    • Author(s)
      Shimegi T, Oyama T, Ohtsuki T, Kurisu G, Kusunoki M, Ui S
    • Journal Title

      Acta Cryst F

      Volume: 70 Issue: 4 Pages: 461-463

    • DOI

      10.1107/s2053230x13032755

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Purification and characterization of a protease from Isaria cicadae2014

    • Author(s)
      Takekawa C, Nakamura K, Homma H, Oyama T
    • Journal Title

      Mushroom Science and Biotechnology

      Volume: 22 Pages: 74-78

    • NAID

      110009863113

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Molecular dynamics study-guided identification of cyclic amine structures as novel hydrophobic tail components of hPPARγ agonists.2014

    • Author(s)
      Y. Tanaka, K. Gamo, T. Oyama, M. Ohashi, M. Waki, K. Matsuno, N. Matsuura, H. Tokiwa, H. Miyachi.
    • Journal Title

      Bioorganic & Medicinal Chemistry Letters

      Volume: 24 Issue: 16 Pages: 4001-4005

    • DOI

      10.1016/j.bmcl.2014.06.023

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structure of the entire stalk region of the dynein motor domain2014

    • Author(s)
      Yosuke Nishikawa, Takuji Oyama, Narutoshi Kamiya, Takahide Kon, Yoko Y. Toyoshima, Haruki Nakamura, Genji Kurisu
    • Journal Title

      Journal of Molecular Biology

      Volume: 426 Issue: 19 Pages: 3232-3245

    • DOI

      10.1016/j.jmb.2014.06.023

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Disordered interdomain region of Gins is important for functional tetramer formation to stimulate MCM helicase in Thermoplasma acidophilum2014

    • Author(s)
      Ogino H, Ishino S, Oyama T, Kohda D, Ishino Y
    • Journal Title

      Biosci Biotechnol Biochem

      Volume: 79 Issue: 3 Pages: 432-438

    • DOI

      10.1080/09168451.2014.982503

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Presentation] 結晶構造から明らかになった古細菌GANのDNA複製でのCMG因子および修復でのヌクレアーゼとしての2つの役割2016

    • Author(s)
      大山拓次、石野園子、白井剛、山上健、永田麻梨子、尾木野弘実、楠木正巳、石野良純
    • Organizer
      第39回日本分子生物学会年会
    • Place of Presentation
      パシフィコ横浜(横浜市西区)
    • Year and Date
      2016-11-30
    • Related Report
      2016 Annual Research Report
  • [Presentation] 大豆イソフラボングルコシルトランスフェラーゼGmIF7GTの結晶構造解析2014

    • Author(s)
      桑名美貴子、楠木正巳、大山拓次、中山亨
    • Organizer
      平成26年度日本結晶学会年会
    • Place of Presentation
      東京大学農学部(東京都文京区)
    • Year and Date
      2014-11-01 – 2014-11-03
    • Related Report
      2014 Research-status Report
  • [Presentation] 大豆イソフラボングルコシルトランスフェラーゼGmIF7GTの構造生物学2014

    • Author(s)
      桑名美貴子、楠木正巳、大山拓次、中山亨
    • Organizer
      第87回日本生化学会年会
    • Place of Presentation
      国立京都国際会館(京都市左京区)
    • Year and Date
      2014-10-15 – 2014-10-18
    • Related Report
      2014 Research-status Report
  • [Remarks] 山梨大学 研究者総覧 大山拓次

    • URL

      http://erdb.yamanashi.ac.jp/rdb/A_DispInfo.Scholar/0/32B8A9CF314A20D1.html

    • Related Report
      2016 Annual Research Report 2015 Research-status Report
  • [Remarks] 研究成果掲載記事(山梨大学生命環境学部HPトピックス)

    • URL

      http://www.les.yamanashi.ac.jp/modules/news/index.php?page=article&storyid=204

    • Related Report
      2016 Annual Research Report 2015 Research-status Report
  • [Remarks] 研究成果掲載記事(山梨大学生命環境学部HPトピックス)

    • URL

      http://www.les.yamanashi.ac.jp/modules/news/index.php?page=article&storyid=232

    • Related Report
      2016 Annual Research Report
  • [Remarks] 研究成果掲載記事(山梨大学NEWS)

    • URL

      http://www.yamanashi.ac.jp/6595

    • Related Report
      2016 Annual Research Report
  • [Remarks] 山梨大学 研究者総覧 大山拓次

    • URL

      http://erdb.yamanashi.ac.jp/rdb/A_DispInfo.Scholar/0/32B8A9CF314A20D1.html

    • Related Report
      2014 Research-status Report

URL: 

Published: 2014-04-04   Modified: 2018-03-22  

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