Crystal structure of the C-terminal domain of envelope protein VP37 from white spot syndrome virus

• Project/Area Number: 20K06238
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 40040:Aquatic life science-related
• Research Institution: Osaka University
• Principal Investigator: Suzuki Mamoru 大阪大学, 蛋白質研究所, 准教授 (40280507)
• Project Period (FY): 2020-04-01 – 2024-03-31
• Project Status: Completed (Fiscal Year 2023)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2022: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2021: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2020: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000)
• Keywords: X線結晶学 / る甲殻 類急性ウイルス血症 / X線結晶構造解析 / 甲殻類急性ウイルス血症

Outline of Research at the Start

甲殻類急性ウイルス血症のVP37および感染関連分子群の大量発現系の構築と精製方法および結晶化条件の探索を行う。結晶が得られれば放射光施設で回折実験を行い、その立体構造を解明する。そして、立体構造情報を元に生化学実験を行い、感染機構を明らかにする。

Outline of Final Research Achievements

Research to determine the 3D structures of infection-associated molecules to elucidate the infection mechanism of crustacean acute viremia has just begun. In this study, we elucidated the X-ray crystal structure of VP37 and proposed a model of its complex with infection-associated VP28. We hope that the results of this study will be used in future studies to elucidate the mechanisms of WSSV infection and the important information base for the prevention and protection of crustacean acute viremia.

Academic Significance and Societal Importance of the Research Achievements

分解能2.51AでVP37のX線結晶構造解析に成功した。

Research Products

• [Int'l Joint Research] King Mongkut's University of Technology(タイ)
• [Int'l Joint Research] King Mongkut's University of Technology(タイ)
• [Int'l Joint Research] King Mongkut's University of Technology/Synchrotron Light Research Institute/Mahidol University(タイ)
• [Int'l Joint Research] King Mongkut's University of Technology/Synchrotron Light Research Institute/Mahidol University(タイ)
• [Journal Article] Oxygen-evolving photosystem II structures during S1-S2-S3 transitions (2024)
  • Author(s): Li Hongjie、Nakajima Yoshiki、Nango Eriko、Owada Shigeki、Yamada Daichi、Tosha Takehiko、Tono Kensuke、Joti Yasumasa、Hatsui Takaki、Yabashi Makina、Kubo Minoru、Iwata So、Isobe Hiroshi、Yamaguchi Kizashi、Suga Michihiro、Shen Jian-Ren
  • Journal Title: Nature Volume: 626 Issue: 7999 Pages: 670-677
  • DOI: 10.1038/s41586-023-06987-5
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Identification of the Acidification Mechanism of the Optimal pH for RNase He1 (2023)
  • Author(s): Takebe Katsuki、Suzuki Mamoru、Sangawa Takeshi、Motoyoshi Naomi、Itagaki Tadashi、Kashima Kana、Uzawa Narikazu、Kobayashi Hiroko
  • Journal Title: Biological and Pharmaceutical Bulletin Volume: 46 Issue: 12 Pages: 1778-1786
  • DOI: 10.1248/bpb.b23-00511
  • ISSN: 0918-6158, 1347-5215
  • Year and Date: 2023-12-01
  • Peer Reviewed
• [Journal Article] Analysis of FctB3 crystal structure and insight into its structural stabilization and pilin linkage mechanisms. (2023)
  • Author(s): Takebe K, Suzuki M, Sangawa T, Kreikemeyer B, Yamaguchi M, Uzawa N, Sumitomo T, Kawabata S, Nakata M.
  • Journal Title: Arch. Microbiol. Volume: 206 Issue: 1 Pages: 4-4
  • DOI: 10.1007/s00203-023-03727-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Time-resolved serial crystallography to track the dynamics of carbon monoxide in the active site of cytochrome c oxidase (2023)
  • Author(s): Safari Cecilia et. al.
  • Journal Title: Science Advances Volume: 9 Issue: 49 Pages: 1-12
  • DOI: 10.1126/sciadv.adh4179
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Neutron Crystallography of a Semiquinone Radical Intermediate of Copper Amine Oxidase Reveals a Substrate-Assisted Conformational Change of the Peptidyl Quinone Cofactor (2023)
  • Author(s): Murakawa Takeshi、Kurihara Kazuo、Shoji Mitsuo、Yano Naomine、Kusaka Katsuhiro、Kawano Yoshiaki、Suzuki Mamoru、Shigeta Yasuteru、Yano Takato、Adachi Motoyasu、Tanizawa Katsuyuki、Okajima Toshihide
  • Journal Title: ACS Catalysis Volume: 13 Issue: 18 Pages: 12403-12413
  • DOI: 10.1021/acscatal.3c02629
  • Peer Reviewed
• [Journal Article] Structural and Computational Analyses of the Unique Interactions of Opicapone in the Binding Pocket of Catechol O-Methyltransferase: A Crystallographic Study and Fragment Molecular Orbital Analyses (2023)
  • Author(s): Takebe Katsuki、Suzuki Mamoru、Kuwada-Kusunose Takao、Shirai Satoko、Fukuzawa Kaori、Takamiya Tomoko、Uzawa Narikazu、Iijima Hiroshi
  • Journal Title: Journal of Chemical Information and Modeling Volume: 63 Issue: 14 Pages: 4468-4476
  • DOI: 10.1021/acs.jcim.3c00331
  • Peer Reviewed
• [Journal Article] Serial femtosecond X-ray crystallography of an anaerobically formed catalytic intermediate of copper amine oxidase (2022)
  • Author(s): Murakawa Takeshi、Suzuki Mamoru、Fukui Kenji、Masuda Tetsuya、Sugahara Michihiro、Tono Kensuke、Tanaka Tomoyuki、Iwata So、Nango Eriko、Yano Takato、Tanizawa Katsuyuki、Okajima Toshihide
  • Journal Title: Acta Crystallographica Section D Structural Biology Volume: 78 Issue: 12 Pages: 1428-1438
  • DOI: 10.1107/s2059798322010385
  • Peer Reviewed / Open Access
• [Journal Article] Structure of thaumatin under acidic conditions: Structural insight into the conformations in lysine residues responsible for maintaining the sweetness after heat-treatment (2022)
  • Author(s): Masuda Tetsuya、Okubo Kyohei、Baba Seiki、Suzuki Mamoru、Tani Fumito、Yamasaki Masayuki、Mikami Bunzo
  • Journal Title: Food Chemistry Volume: 389 Pages: 132996-132996
  • DOI: 10.1016/j.foodchem.2022.132996
  • Peer Reviewed / Open Access
• [Journal Article] Microcrystal preparation for serial femtosecond X-ray crystallography of bacterial copper amine oxidase (2021)
  • Author(s): Murakawa Takeshi、Suzuki Mamoru、Arima Toshi、Sugahara Michihiro、Tanaka Tomoyuki、Tanaka Rie、Iwata So、Nango Eriko、Tono Kensuke、Hayashi Hideyuki、Fukui Kenji、Yano Takato、Tanizawa Katsuyuki、Okajima Toshihide
  • Journal Title: Acta Crystallographica Section F Structural Biology Communications Volume: 77 Issue: 10 Pages: 356-363
  • DOI: 10.1107/s2053230x21008967
  • Peer Reviewed
• [Journal Article] Crystal structure of the C-terminal domain of envelope protein VP37 from white spot syndrome virus reveals sulphate binding sites responsible for heparin binding (2021)
  • Author(s): Somsoros Wasusit、Sangawa Takeshi、Takebe Katsuki、Attarataya Jakrada、Wongprasert Kanokpan、Senapin Saengchan、Rattanarojpong Triwit、Suzuki Mamoru、Khunrae Pongsak
  • Journal Title: Journal of General Virology Volume: 102 Issue: 6
  • DOI: 10.1099/jgv.0.001611
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Capturing structural changes of the S1 to S2 transition of photosystem II using time-resolved serial femtosecond crystallography (2021)
  • Author(s): H Li, Y Nakajima, T Nomura, M Sugahara, S Yonekura, SK Chan, T Nakane, T Yamane, Y Umena, M Suzuki, T Masuda, T Motomura, H Naitow, Y Matsuura, T Kimura, K Tono, S Owada, Y Joti, R Tanaka, E Nango, F Akita, M Kubo, S Iwata, JR Shen and M Suga
  • Journal Title: IUCrJ Volume: 8 Issue: 3 Pages: 431-443
  • DOI: 10.1107/s2052252521002177
  • NAID: 120007037379
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Crystal Structure of Catechol <i>O</i>-Methyltransferase Complexed with Nitecapone (2020)
  • Author(s): Iijima Hiroshi、Takebe Katsuki、Suzuki Mamoru、Kobayashi Hiroko、Takamiya Tomoko、Saito Hiroaki、Niwa Norio、Kuwada-Kusunose Takao
  • Journal Title: Chemical and Pharmaceutical Bulletin Volume: 68 Issue: 5 Pages: 447-451
  • DOI: 10.1248/cpb.c20-00011
  • NAID: 130007838793
  • ISSN: 0009-2363, 1347-5223
  • Year and Date: 2020-05-01
  • Peer Reviewed
• [Journal Article] Viscosity-adjustable grease matrices for serial nanocrystallography (2020)
  • Author(s): Sugahara Michihiro、Motomura Koji、Suzuki Mamoru、Masuda Tetsuya、Joti Yasumasa、Numata Keiji、Tono Kensuke、Yabashi Makina、Ishikawa Tetsuya
  • Journal Title: Scientific Reports Volume: 10 Issue: 1 Pages: 1371-1371
  • DOI: 10.1038/s41598-020-57675-7
  • Peer Reviewed / Open Access
• [Journal Article] Neutron crystallography of copper amine oxidase reveals keto/enolate interconversion of the quinone cofactor and unusual proton sharing (2020)
  • Author(s): Takeshi Murakawa, Kazuo Kurihara, Mitsuo Shoji, Chie Shibazaki, Tomoko Sunami, Taro Tamada, Naomine Yano, Taro Yamada, Katsuhiro Kusaka, Mamoru Suzuki, Yasuteru Shigeta, Ryota Kuroki, Hideyuki Hayashi, Takato Yano, Katsuyuki Tanizawa, Motoyasu Adachi, Toshihide Okajima
  • Journal Title: Proceedings of the National Academy of Sciences Volume: 印刷中 Issue: 20 Pages: 10818-10824
  • DOI: 10.1073/pnas.1922538117
  • Peer Reviewed / Open Access
• [Presentation] Hyaluronidase in Streptococcus pyogenes - analysis based on structural biology and molecular phylogenetics (2023)
  • Author(s): Kotaro Higashi, Masaya Yamaguchi, Katsuki Takebe, Masanobu Nakata , Tomoko Sumitomo, Mamoru Suzuki, Victor Nizet, Shigetada Kawabata
  • Organizer: Glycobiology 2023: Transformative Advances in the Biological Functions of Glycans
  • Int'l Joint Research
• [Presentation] カテコールO-メチル転移酵素の配座構造の変化 (2023)
  • Author(s): 飯島 洋、武部 克希、鈴木 守、桑田-楠瀬 隆生、髙宮 知子、鵜澤 成一
  • Organizer: 日本薬学会第143年会
• [Presentation] ヤマブシタケ由来RNase He1の至適ｐHに関与するアミノ酸残基の検討 (2023)
  • Author(s): 小林 弘子、武部 克希、元吉 尚美、板垣 正、鵜澤 成一、鈴木 守
  • Organizer: 日本薬学会第143年会
• [Presentation] Investigation of hydrogen bond network in the active center of catechol O-methyltransferase by X-ray crystallography and FMO method (2022)
  • Author(s): Katsuki Takebe, Tomoko Shirai, Yuma Handa, Kaori Fukuzawa, Mamoru Suzuki, Takao K
  • Organizer: 情報計算化学生物学会(CBI学会)
• [Presentation] Molecular movie of the catalytic reaction of bacterial copper amine oxidase conducted by mix and inject serial femtosecond X ray crystallography (2022)
  • Author(s): Takeshi Murakawa , Mamoru Suzuki, Kenji Fukui, Tetuya Masuda, Ikuko Miyahara, Takehiko Tosha, Takato Yano, So Iwata, Eriko Nango, Katsuyuki Tanizawa, Toshihide Okajima
  • Organizer: Molecular Movies International Symposium 2022
  • Int'l Joint Research
• [Presentation] ヤマブシタケ由来RNase He1の3’-GMP複合体のX線結晶構造解析 (2022)
  • Author(s): 小林弘子、寒川 剛 武部克希 元吉尚美、板垣正、鈴木守
  • Organizer: 日本薬学会第142年会
• [Presentation] COMT（カテコールO-メチル基転移酵素）-新規阻害剤の複合体の構造解析: Opicaponeは基質（SAM）, 生成物（SAH）とも安定な複合体を形成する (2022)
  • Author(s): 武部 克希、桑田（楠瀬） 隆生、鈴木 守、髙宮 知子、鵜澤 成一、飯島 洋
  • Organizer: 日本薬学会第142年会
• [Presentation] 賦活化化合物によるCOMTの生成物阻害の解除機構：結晶構造解析による検討 (2022)
  • Author(s): 飯島 洋、武部 克希、桑田（楠瀬） 隆生、鈴木 守、髙宮 知子、鵜澤 成一
  • Organizer: 日本薬学会第142年会
• [Presentation] 化膿レンサ球菌の不活性型ヒアルロン酸分解酵素の結晶構造解析と活性型変異体の構造予測 (2021)
  • Author(s): 東 孝太郎, 山口 雅也，中田 匡宣，武部 克希，住友 倫子，鈴木 守，川端 重忠
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• [Presentation] 二液混合シリアルフェムト秒結晶構造解析による酵素反応及び構造変化追跡 (2021)
  • Author(s): 南後恵理子、Fangjia Luo、木村哲就 、菅原道泰、中根崇智 、鈴木守 、桝田哲哉 、溝端栄一、登野健介、岩田想
  • Organizer: 日本結晶学会令和3年度年会
• [Presentation] 結晶構造解析に基づく化膿レンサ球菌におけるヒアルロン酸分解酵素の分子機構解明 (2021)
  • Author(s): 東 孝太郎, 山口 雅也，中田 匡宣，武部 克希，住友 倫子，鈴木 守，川端 重忠
  • Organizer: 第43回分子生物学会
• [Presentation] 歯周病細菌叢の病原性を抑える試み (2021)
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  • Organizer: 第43回分子生物学会
• [Presentation] COMT/阻害剤複合体の結晶構造解析及び、量子化学計算による相互作用解析 (2020)
  • Author(s): 武部克希、福澤薫、鈴木守、楠瀬隆生、鵜澤成一、飯島洋
  • Organizer: 第48回構造活性相関シンポジウム
• [Presentation] 化膿レンサ球菌におけるヒアルロン酸分解酵素の分子系統解析および結晶構造解析 (2020)
  • Author(s): 東 孝太郎，武部 克希，山口 雅也，住友 倫子，中田 匡宣，鈴木 守，川端 重忠
  • Organizer: 第43回分子生物学会