Structural analysis of cytochrome bd oxidase complex with substrate

• Project/Area Number: 15K18488
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Osaka University
• Principal Investigator: Nakaniwa Tetsuko 大阪大学, たんぱく質研究所, 特別研究員(RPD) (80569070)
• Research Collaborator: KURISU GENJI 大阪大学, 蛋白質研究所, 教授 (90294131) ; TANAKA HIDEAKI 大阪大学, 蛋白質研究所, 准教授 (40346169)
• Project Period (FY): 2015-04-01 – 2018-03-31
• Project Status: Completed (Fiscal Year 2017)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2017: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000); Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2015: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
• Keywords: 呼吸鎖電子伝達系 / シトクロム末端酸化酵素 / 構造生物学 / 結晶構造解析 / 呼吸鎖複合体 / 膜タンパク質複合体

Outline of Final Research Achievements

The cytochrome bd oxidases (Cytbd) are terminal oxidases that reduce molecular oxygen to water, avoiding the production of reactive oxygen species. In addition to their contribution to the proton motive force, they mediate viability under oxygen-related stress conditions. Here I aimed at the decision of the Cytbd complex structure with substrate. In this study, I made cocrystal of high quality and carried out the X-ray measurement that held the damage of the crystal. As a result, I succeeded in collecting the data of the highest resolution of 4.8A. It was determined in the initial phase by molecular replacement and then carried out the structure construction and refinement. However, it was not possible to obtain a novel structure knowledge.

Research Products

• [Journal Article] A substrate-bound structure of cyanobacterial biliverdin reductase identifies stacked substrates as critical for activity (2017)
  • Author(s): Haruna Takao, Kei Hirabayashi, Yuki Nishigaya, Haruna Kouriki, Tetsuko Nakaniwa, Yoshinori Hagiwara, Jiro Harada, Hideaki Sato, Toshimasa Yamazaki, Yoichi Sakakibara, Masahito Suiko, Yujiro Asada, Yasuhiro Takahashi, Ken Yamamoto, Keiichi Fukuyama, Masakazu Sugishima, and Kei Wada
  • Journal Title: Nat. Commun. Volume: 8 Issue: 1 Pages: 1-10
  • DOI: 10.1038/ncomms14397
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of Protein Kinase CK2 Inhibitors using Solvent Dipole Ordering Virtual Screening. (2015)
  • Author(s): Isao Nakanishi, Katsumi Murata, Naoya Nagata, Masakuni Kurono, Takayoshi Kinoshita, Misato Yasue, Takako Miyazaki, Yoshinori Takei, Shinya Nakamura, Atsushi Sakurai, Nobuko Iwamoto, Keiji Nishiwaki, Tetsuko Nakaniwa, Yusuke Sekiguchi, Akira Hirasawa, Gozoh Tsujimoto, and Kazuo Kitaura.
  • Journal Title: Eur. J. Med. Chem. Volume: 96 Pages: 396-404
  • DOI: 10.1016/j.ejmech.2015.04.032
  • Peer Reviewed
• [Presentation] CK 2a1-hemateinの結合を変化させる間接的要因 (2017)
  • Author(s): 露口 正人、平澤 明、仲庭 哲津子、櫻井 淳史、仲西 功、木下 誉富
  • Organizer: 2017年度 日本薬学会年会
  • Place of Presentation: 仙台国際センター（宮城県仙台市）
  • Year and Date: 2017-03-24
• [Presentation] タイプ１型光合成反応中心のX線結晶構造解析 (2017)
  • Author(s): 伏見こころ、仲庭哲津子、武藤梨沙、安田亜矢、安藤俊介、田中秀明、大岡宏造、栗栖源嗣
  • Organizer: 光合成細菌セミナー
• [Presentation] 深所型緑藻における新規光合成アンテナの再構成法の確立 (2017)
  • Author(s): 仲庭哲津子、Ratana Charoenwattanasatien、乗岡尚子、東田怜、山野奈美、狩野竜一、藤原健太郎、大滝宏代、田中秀明、藤井律子、栗栖源嗣
  • Organizer: 光合成細菌セミナー
• [Presentation] CK2a1-hemateinの結合を変化させる間接的要因 (2017)
  • Author(s): 露口正人、平澤明、仲庭哲津子、櫻井淳史、仲西功、木下誉富
  • Organizer: 第17回日本蛋白質科学会年会
• [Presentation] CK2α2の高分解能X線結晶構造解析 (2016)
  • Author(s): 露口 正人、仲庭 哲津子、仲西 功、木下 誉富
  • Organizer: 日本結晶学会平成28年度年会
  • Place of Presentation: 茨城県県民文化センター（茨城県水戸市）
  • Year and Date: 2016-11-17
• [Presentation] Crystal structure of CK2α2 in the new crystal form. (2016)
  • Author(s): Masato Tsuyuguchi, Tetsuko Nakaniwa, Isao Nakanishi, Takayoshi Kinoshita
  • Organizer: 8th International Conference on Protein Kinase CK2
  • Place of Presentation: Germany（Homburg）
  • Year and Date: 2016-09-06
  • Int'l Joint Research
• [Presentation] His160のコンホメーション変化とhemateinによるATP非拮抗型CK2α1阻害の関係 (2016)
  • Author(s): 露口 正人、平澤 明、仲庭 哲津子、櫻井 淳史、仲西 功、木下 誉富
  • Organizer: 第16回日本蛋白質科学会年会
  • Place of Presentation: 福岡国際会議場（福岡県福岡市）
  • Year and Date: 2016-06-07
• [Presentation] CK2 サブタイプ間で異なる四環性化合物の阻害作用機序の解明 (2015)
  • Author(s): 露口 正人、平澤 明、仲庭 哲津子、櫻井 淳史、仲西 功、木下 誉富
  • Organizer: 日本結晶学会平成27年度年会
  • Place of Presentation: 大阪府立大学(大阪府堺市)
  • Year and Date: 2015-10-17
• [Presentation] tructural basis for producing CK2α1- specific inhibitors: Crystal structures of hematein with CK2α 1 and CK2α2 (2015)
  • Author(s): 露口 正人、平澤 明、仲庭 哲津子、櫻井 淳史、仲西 功、木下 誉富
  • Organizer: 日本薬学会構造活性相関シンポジウム
  • Place of Presentation: 新潟日報メディアシップ(新潟県新潟市)
  • Year and Date: 2015-09-27
• [Presentation] CK2サブタイプ間で異なるhemateinの阻害作用メカニズムの解明 (2015)
  • Author(s): 露口 正人、平澤 明、仲庭 哲津子、櫻井 淳史、仲西 功、木下 誉富
  • Organizer: 第15回日本タンパク質科学会年会
  • Place of Presentation: 徳島市あわぎんホール(徳島県徳島市)
  • Year and Date: 2015-06-24