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Structural analysis for photosystem II in the intermediate Si-state by using X-ray free electron laser pulses

Research Project

Project/Area Number 16H06162
Research Category

Grant-in-Aid for Young Scientists (A)

Allocation TypeSingle-year Grants
Research Field Structural biochemistry
Research InstitutionOkayama University

Principal Investigator

Suga Michihiro  岡山大学, 異分野基礎科学研究所, 准教授 (60634920)

Research Collaborator Shen Jian-Ren  
Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥24,570,000 (Direct Cost: ¥18,900,000、Indirect Cost: ¥5,670,000)
Fiscal Year 2018: ¥4,680,000 (Direct Cost: ¥3,600,000、Indirect Cost: ¥1,080,000)
Fiscal Year 2017: ¥5,850,000 (Direct Cost: ¥4,500,000、Indirect Cost: ¥1,350,000)
Fiscal Year 2016: ¥14,040,000 (Direct Cost: ¥10,800,000、Indirect Cost: ¥3,240,000)
Keywords光化学系 / 光合成 / X線自由電子レーザー / 動的構造 / ダイナミクス / 膜タンパク質 / 人工光合成 / 量子ビーム / X線自由レーザー / X線自由電子レーザー / X線結晶構造解析
Outline of Final Research Achievements

Photosystem II (PSII) catalyzes photo-oxidation of water into dioxygen through an S-state cycle of the oxygen evolving complex (OEC). The structure of PSII has been analyzed at resolutions higher than 2.0A by using X-ray as well as XFEL. The mechanism of O=O bond formation, however, remains obscure owing to the lack of intermediate-state structures determined at atomic resolution. We prepared PSII in the S3 state by providing two-flash illumination into micro-sized crystals at room temperature and determined the structure at 2.35A resolution by using an XFEL. An isomorphous difference Fourier map between the two-flash-illuminated and dark-adapted states revealed apparent structural changes. Among them, the insertion of a new oxygen atom O6 close to the putative substrate oxo-bridge O5 was observed. We proposed the mechanism of O=O bond formation between O5 and O6. The findings provide a structural basis for the mechanism of oxygen evolution.

Academic Significance and Societal Importance of the Research Achievements

光化学系IIは可視光による水分子の酸化反応を触媒することのできる唯一の天然触媒である。今回X線自由電子レーザーを利用した反応中間体の構造解析によりO6とよばれる水分子が触媒部分に取り入れられることで水分解反応が起こるということを実験的に観察し、触媒反応の基本原理を世界で初めて実証した。この知見は再生可能でクリーンなエネルギーを作り出す人工光合成研究への応用も期待できる。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (23 results)

All 2019 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (7 results) (of which Int'l Joint Research: 5 results,  Peer Reviewed: 7 results,  Open Access: 4 results,  Acknowledgement Compliant: 2 results) Presentation (12 results) (of which Int'l Joint Research: 2 results,  Invited: 12 results) Remarks (2 results)

  • [Int'l Joint Research] Key Laboratory of Photobiology/Institute of Botany/Chinese Academy of Science(中国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] フランス国立科学研究センター(フランス)

    • Related Report
      2017 Annual Research Report
  • [Journal Article] Structural basis for blue-green light harvesting and energy dissipation in diatoms2019

    • Author(s)
      Wang Wenda、Yu Long-Jiang、Xu Caizhe、Tomizaki Takashi、Zhao Songhao、Umena Yasufumi、Chen Xiaobo、Qin Xiaochun、Xin Yueyong、Suga Michihiro、Han Guangye、Kuang Tingyun、Shen Jian-Ren
    • Journal Title

      Science

      Volume: 363 Issue: 6427

    • DOI

      10.1126/science.aav0365

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Thylakoid membrane lipid sulfoquinovosyl-diacylglycerol (SQDG) is required for full functioning of photosystem II in Thermosynechococcus elongatus2018

    • Author(s)
      Nakajima, Y., Umena, Y., Nagao, R., Endo, K., Kobayashi, K., Akita, F., Suga, M., Wada, H., Noguchi, T., Shen, J.-R.
    • Journal Title

      J. Biol. Chem.

      Volume: 293 Issue: 38 Pages: 14786-14797

    • DOI

      10.1074/jbc.ra118.004304

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Fourier Transform Infrared Analysis of the S-State Cycle of Water Oxidation in the Microcrystals of Photosystem II2018

    • Author(s)
      Kato Yuki、Akita Fusamichi、Nakajima Yoshiki、Suga Michihiro、Umena Yasufumi、Shen Jian-Ren、Noguchi Takumi
    • Journal Title

      The Journal of Physical Chemistry Letters

      Volume: 9 Issue: 9 Pages: 2121-2126

    • DOI

      10.1021/acs.jpclett.8b00638

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Structure of photosynthetic LH1-RC supercomplex at 1.9 A resolution2018

    • Author(s)
      Yu Long-Jiang、Suga Michihiro、Wang-Otomo Zheng-Yu、Shen Jian-Ren
    • Journal Title

      Nature

      Volume: 556 Issue: 7700 Pages: 209-213

    • DOI

      10.1038/s41586-018-0002-9

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Crystal structure and redox properties of a novel cyanobacterial heme protein with a His/Cys heme axial ligation and a Per-Arnt-Sim (PAS)-like domain2017

    • Author(s)
      Motomura Taiki、Suga Michihiro、Hienerwadel Rainer、Nakagawa Akiko、Lai Thanh-Lan、Nitschke Wolfgang、Kuma Takahiro、Sugiura Miwa、Boussac Alain、Shen Jian-Ren
    • Journal Title

      Journal of Biological Chemistry

      Volume: 292 Issue: 23 Pages: 9599-9612

    • DOI

      10.1074/jbc.m116.746263

    • NAID

      120006473741

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Light-induced structural changes and the site of O=O bond formation in PSII caught by XFEL.2017

    • Author(s)
      Suga, M.†, Akita, F.†, Sugahara, M.†, Kubo, M.†, Nakajima, Y.† et al. (†equal contribution)(38人中1番目)
    • Journal Title

      Nature

      Volume: 543 Issue: 7643 Pages: 131-135

    • DOI

      10.1038/nature21400

    • NAID

      120006344935

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Large-scale QM/MM calculations of the CaMn4O5 cluster in the S3 state of the oxygen evolving complex of photosystem II. Comparison between water-inserted and no water-inserted structures.2017

    • Author(s)
      Shoji M, Isobe H, Nakajima T, Shigeta Y, Suga M, Akita F, Shen JR and *Yamazaki K.
    • Journal Title

      Faraday Discussions

      Volume: 198 Pages: 83-106

    • DOI

      10.1039/c6fd00230g

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
  • [Presentation] 光合成光化学系IIの反応中間体の結晶構造と酸素発生反応機構2018

    • Author(s)
      菅倫寛, 沈建仁 (招待講演)
    • Organizer
      第18回日本蛋白質科学会年会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Structure of oxygen evolving photosystem II and possible mechanism for the O=O bond formation.2018

    • Author(s)
      Michi Suga (invited talk)
    • Organizer
      SACLA Users’ meeting 2018
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structure of oxygen evolving photosystem II and possible mechanism for the O=O bond formation.2018

    • Author(s)
      Michi Suga, Jian-Ren Shen (invited talk)
    • Organizer
      The 56th annual meeting of the biophysical society of Japan
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] X線自由電子レーザーにより明らかにされた光学系IIの光励起した反応中間体構造および水分解・酸素発生の反応機構2017

    • Author(s)
      菅 倫寛,秋田総理,菅原道泰,久保 稔,中島芳樹,岩田 想,沈 建仁
    • Organizer
      第17回日本蛋白質科学会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] X線自由電子レーザーにより明らかにされた光学系IIの水分解・酸素発生の反応機構2017

    • Author(s)
      菅 倫寛
    • Organizer
      分子研研究会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] X線自由電子レーザーにより明らかにされた光学系IIの光励起した反応中間体構造および水分解・酸素発生の反応機構2017

    • Author(s)
      菅 倫寛,秋田総理,菅原道泰,久保 稔,中島芳樹,岩田 想,沈 建仁
    • Organizer
      ConBio2017
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] X線自由電子レーザーにより明らかにされた光学系IIの水分解・酸素発生の反応機構2017

    • Author(s)
      菅 倫寛,沈 建仁
    • Organizer
      日本生体エネルギー研究会第43回討論会
    • Related Report
      2017 Annual Research Report
    • Invited
  • [Presentation] 光合成蛋白質の構造と機能に関する結晶学的研究2017

    • Author(s)
      菅 倫寛
    • Organizer
      第58回日本植物生理学会授賞式
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 光合成膜タンパク質複合体の構造機能研究.2017

    • Author(s)
      菅 倫寛
    • Organizer
      第169委員会第52回研究会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 高等植物光化学系I-光捕集アンテナI超複合体におけるエネルギー伝達経路の構造基盤2016

    • Author(s)
      菅 倫寛、Xiaochun Qin, Tingyun Kuang, 沈 建仁
    • Organizer
      第7回日本光合成学会年会およびシンポジウム
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Structural studies of photosystems2016

    • Author(s)
      Michi Suga
    • Organizer
      Finnish-Japanese symposium 2016 Integration of photosynthesis with cellular metabolism: towards suitable biochemistry.
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Structure of an intermediate S-state of photosystem II reveled by XFELs2016

    • Author(s)
      Michi Suga
    • Organizer
      第54回日本生物物理学会年会
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Remarks] 反応中心LH1-RC超複合体の構造解析についてプレス発表,日刊工業新聞,読売新聞,山陽新聞で紹介

    • URL

      https://www.okayama-u.ac.jp/tp/release/release_id535.html

    • Related Report
      2017 Annual Research Report
  • [Remarks] 光化学系IIの構造解析についてプレス発表,日経新聞,朝日新聞,読売新聞,毎日新聞,山陽新聞などで紹介

    • URL

      https://www.okayama-u.ac.jp/tp/release/release_id448.html

    • Related Report
      2016 Annual Research Report

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Published: 2016-04-21   Modified: 2020-03-30  

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