Structural analysis of novel type 6 secretion apparatus proteins

• Project/Area Number: 21770164
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Biophysics
• Research Institution: Tokyo Institute of Technology
• Principal Investigator: KANAMARU Shuji 東京工業大学, 生命理工学研究科, 助教 (50376951)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥3,380,000 (Direct Cost: ¥2,600,000、Indirect Cost: ¥780,000); Fiscal Year 2011: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2010: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2009: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
• Keywords: グラム陰性菌 / 分泌装置 / バクテリオファージ / 構造解析 / T6SS / βヘリックス / VgrG

Research Abstract

To determine the crystal structure of VgrG protein of Type 6 secresion apparatus from E. coli O157 and E. coli CFT073, over-expression vectors for both full-length and C-terminal domain of VgrG were constructed. We succeeded in establish the purification methods for VgrG from E. coli O157. Purified protein was treated with trypsin to get stable VgrG1^M467-his. This VgrG1^M467-his was examined thousands of crystallization condition. One of the conditions gave nice crystal formation for structure determination. Now we are trying get isomorphous heavy atom derivatives for phase determination. Moreover, we are going to establish other VgrG purification strategy.

Research Products

• [Journal Article] Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus (2012)
  • Author(s): 行、高橋宏樹
  • Journal Title: J Virol Volume: 86 Pages: 746-56
  • Peer Reviewed
• [Journal Article] Crystallographic analysis reveals octamerization of viroplasm matrix protein P9-1 of Rice black streaked dwarf virus (2012)
  • Author(s): Akita F, Higashiura A, Shimizu T, Pu Y, Suzuki M, Uehara-Ichiki T, Sasaya T, Kanamaru S, Arisaka F, Tsukihara T, Nakagawa A, Omura T
  • Journal Title: J Virol Volume: 86(2) Issue: 2 Pages: 746-756
  • DOI: 10.1128/jvi.00826-11
  • Peer Reviewed
• [Journal Article] Dual modification of a triple-stranded beta-helix nanotube with Ru and Re metal complexes to promote photocatalytic reduction of CO2 (2011)
  • Author(s): Yokoi, N., Miura, Y., Huang, C. Y., Takatani, N., Inaba, H., Koshiyama, T., Kanamaru, S., Arisaka, F., Watanabe, Y., Kitagawa, S. & Ueno, T.
  • Journal Title: Chem Commun(Camb) Volume: 47 Pages: 2074-6
  • Peer Reviewed
• [Journal Article] Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing (2011)
  • Author(s): Nishima, W., Kanamaru, S., Arisaka, F. & Kitao, A.
  • Journal Title: J Am Chem Socl Volume: 33 Pages: 13571-6
  • Peer Reviewed
• [Journal Article] コンポジション・グラジエント法を用いた多角度光散乱装置による分子間相互作用解析 (2011)
  • Author(s): 金丸周司
  • Journal Title: 生物工学会誌 Volume: 89 Pages: 378-380
• [Journal Article] Screw motion regulates multiple functions of T4 phage protein gene product 5 during cell puncturing (2011)
  • Author(s): Nishima W, Kanamaru S, Arisaka F, Kitao A
  • Journal Title: J Am Chem Soc Volume: 133(34) Issue: 34 Pages: 13571-13576
  • DOI: 10.1021/ja204451g
  • Peer Reviewed
• [Journal Article] Dual modification of a triple-stranded β-helix nanotube with Ru and Re metal complexes to promote photocatalytic reduction of CO(2) (2011)
  • Author(s): Yokoi N, Miura Y, Huang CY, Takatani N, Inaba H, Koshiyama T, Kanamaru S, Arisaka F, Watanabe Y, Kitagawa S, Ueno T
  • Journal Title: Chem Commun (Camb) Volume: 47(7) Issue: 7 Pages: 2074-2076
  • DOI: 10.1039/c0cc03015e
  • Peer Reviewed
• [Journal Article] Dual modification of a triple-stranded β-helix nanotube with Ru and Remetal complexes to promote photocatalytic reduction of CO2. (2011)
  • Author(s): Yokoi N, Miura Y, Huang CY, Takatani N, Inaba H, Koshiyama T, Kanamaru S, Arisaka F, Watanabe Y, Kitagawa S, Ueno T.
  • Journal Title: Chem Commun (Camb) Volume: 47 Pages: 2074-2076
  • Peer Reviewed
• [Journal Article] Construction of robust bio-nanotubes using the controlled self-assembly of component proteins of bacteriophage T4 (2010)
  • Author(s): Yokoi, N., Inaba, H., Terauchi, M., Stieg, A. Z., Sanghamitra, N. J., Koshiyama, T., Yutani, K., Kanamaru, S., Arisaka, F., Hikage, T., Suzuki, A., Yamane, T., Gimzewski, J. K., Watanabe, Y., Kitagawa, S. & Ueno, T.
  • Journal Title: Small Volume: 6 Pages: 1873-9
  • Peer Reviewed
• [Journal Article] The baseplate wedges of bacteriophage T4 spontaneously assemble into hubless baseplate-like structure in vitro (2010)
  • Author(s): Yap, M. L., Mio, K., Leiman, P. G., Kanamaru, S. & Arisaka, F.
  • Journal Title: J Mol Biol Volume: 395 Pages: 349-60
  • Peer Reviewed
• [Journal Article] Sequential assembly of the wedge of the baseplate of phage T4 in the presence and absence of gp11 as monitored by analytical ultra-centrifugation (2010)
  • Author(s): Yap, M. L., Mio, K., Ali, S., Minton, A., Kanamaru, S. & Arisaka, F.
  • Journal Title: Macromol Biosci Volume: 10 Pages: 808-13
  • Peer Reviewed
• [Journal Article] Purification and characterization of acetophenone reductase with excellent enantioselectivity from Geotrichum candidum NBRC 4597 (2010)
  • Author(s): Nakata, Y., Fukae, T., Kanamori, R., Kanamaru, S. & Matsuda, T.
  • Journal Title: Appl Microbiol Biotechnol Volume: 86 Pages: 625-31
  • Peer Reviewed
• [Journal Article] Morphogenesis of the T4 tail and tail fibers (2010)
  • Author(s): Leiman, P. G., Arisaka, F., van Raaij, M. J., Kostyuchenko, V. A., Aksyuk, A. A., Kanamaru, S. & Rossmann, M. G.
  • Journal Title: Virol J Volume: 355
  • Peer Reviewed
• [Journal Article] Zernike phase contrast cryo-electron tomography (2010)
  • Author(s): Danev, R., Kanamaru, S., Marko, M. & Nagayama, K.
  • Journal Title: Struct Biol Volume: 171 Pages: 174-81
  • Peer Reviewed
• [Journal Article] Sequential assembly of the wedge of the baseplate of phage T4 in the presence and absence of gp11 as monitored by analytical ultracentrifugation. (2010)
  • Author(s): Yap ML, Mio K, Ali S, Minton A, Kanamaru S, Arisaka F.
  • Journal Title: Macromol Biosci. Volume: 10 Pages: 808-813
  • Peer Reviewed
• [Journal Article] Zernike phase contrast cryo-electron tomography. (2010)
  • Author(s): Danev R, Kanamaru S, Marko M, Nagayama K.
  • Journal Title: J Struct Biol. Volume: 171 Pages: 174-181
  • Peer Reviewed
• [Journal Article] Construction of robust bio-nanotubes using the controlled self-assembly of component proteins of bacteriophage T4. (2010)
  • Author(s): Yokoi N, Inaba H, Terauchi M, Stieg AZ, Sanghamitra NJ, Koshiyama T, Yutani K, Kanamaru S, Arisaka F, Hikage T, Suzuki A, Yamane T, Gimzewski JK, Watanabe Y, Kitagawa S, Ueno T.
  • Journal Title: Small Volume: 6 Pages: 1873-1879
  • Peer Reviewed
• [Journal Article] Morphogenesis of the T4 tail and tail fibers. (2010)
  • Author(s): Leiman PG, Arisaka F, van Raaij MJ, Kostyuchenko VA, Aksyuk AA, Kanamaru S, Rossmann MG.
  • Journal Title: Virol J. Volume: 7 Pages: 355-382
  • Peer Reviewed
• [Journal Article] Purification and characterization of acetophenone reductase with excellent enantioselectivity from Geotrichum candidum NBRC 4597 (2010)
  • Author(s): Y Nakata, T Fukae, R Kanamori, S Kanamaru, T Matsuda
  • Journal Title: Applied microbiology and biotechnology 86 Pages: 625-631
  • Peer Reviewed
• [Journal Article] The baseplate wedges of bacteriophage T4 spontaneously assemble into hubless baseplate-like structure in vitro (2010)
  • Author(s): ML Yap, K Mio, PG Leiman, S Kanamaru, F Arisaka
  • Journal Title: Journal of molecular biology 395 Pages: 349-360
  • Peer Reviewed
• [Journal Article] Construction of an energy transfer system in the bio-nanocup space by heteromeric assembly of gp27 and gp5 proteins isolated from bacteriophage T4 (2009)
  • Author(s): Koshiyama, T., Ueno, T., Kanamaru, S., Arisaka, F. & Watanabe, Y.
  • Journal Title: Org Biomol Chem Volume: 7 Pages: 2649-54
  • Peer Reviewed
• [Journal Article] Structural similarity of tailed phages and pathogenic bacterial secretionsy stems (2009)
  • Author(s): Kanamaru, S.
  • Journal Title: Proc Natl Acad Sci U S A Volume: 106 Pages: 4067-8
  • Peer Reviewed
• [Journal Article] Structural similarity of tailed phages and pathogenic bacterial secretion systems (2009)
  • Author(s): S Kanamaru
  • Journal Title: Proceedings of the National Academy of Sciences of the United States of America 106 Pages: 4067-4068
  • Peer Reviewed
• [Journal Article] Construction of an energy transfer system in the bio-nanocup space by heteromeric assembly of gp27 and gp5 proteins isolated from bacteriophage T4 (2009)
  • Author(s): T Koshiyama, T Ueno, S Kanamaru, F Arisaka, Y Watanabe
  • Journal Title: Organic & biomolecular chemistry 7 Pages: 2649-2654
  • Peer Reviewed
• [Presentation] T4ファージSpsckle蛋白質によるgp5テイルリゾチームの溶菌阻害メカニズム (2011)
  • Author(s): 内田一也、金丸周司、有坂文雄
  • Organizer: 第10回微生物研究会
  • Place of Presentation: 千葉大学松戸キャンパス
  • Year and Date: 2011-11-12
• [Presentation] Crystal structure reveals how spackle protein(gp61. 3) inhibits lysozyme activity of gp5 tail lysozyme from bacteriophage T4 (2011)
  • Author(s): Shuji Kanamaru
  • Organizer: XXIInd Biennial Conference on Phage/Virus Assembly
  • Place of Presentation: The Marine Sciences Institute
  • Year and Date: 2011-10-14
• [Presentation] コンポジション・グラジエント法を用いた多角度光散乱装置による分子間相互作用解析 (2011)
  • Author(s): 金丸周司
  • Organizer: 第1回生体分子相互作用解析ワークショップ
  • Place of Presentation: 東京
  • Year and Date: 2011-03-10
• [Presentation] T4ファージのアンチホーリンによるホーリンの凝集抑制と溶菌阻止メカニズム (2011)
  • Author(s): 伊藤悠太、金丸周司、有坂文雄
  • Organizer: 第84回日本生化学会大会
  • Place of Presentation: 国立京都国際会館
• [Presentation] T4ファージgp7C末端フラグメントの基盤ウェッジ形成における役割 (2011)
  • Author(s): 伊藤豪、金丸周司、有坂文雄
  • Organizer: 第49回日本生物物理学会年会
  • Place of Presentation: 兵庫県立大学・姫路書写キャンパス
• [Presentation] Protein-protein interaction analysis by composition gradient multiangle light scattering(CG-MALS) (2011)
  • Author(s): 金丸周司
  • Organizer: 第11回蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポパーク
• [Presentation] Protein-protein interaction analysis by composition gradient multiangle light scattering(CG-MALS) (2011)
  • Author(s): 金丸周司
  • Organizer: 第11回蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポパーク(招待講演)
• [Presentation] Crystal structure reveals how spackle protein (gp61.3) inhibits lysozyme activity of gp5 tail lysozyme from bacteriophage T4 (2011)
  • Author(s): Shuji Kanamaru
  • Organizer: XXIInd Biennial Conference on Phage/Virus Assembly
  • Place of Presentation: The Marine Sciences Institute
• [Presentation] Identification of the protein components in the baseplate hub assembly of bacteriophage T4 (2010)
  • Author(s): 金丸周司、愛木健人、有坂文雄
  • Organizer: 第83回日本生化学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2010-12-09
• [Presentation] Expression and characterization of the baseplate wedge proteins gp53 and gp25 of bacteriophage T4 (2010)
  • Author(s): 門崎泰憲、金丸周司、有坂文雄
  • Organizer: 第83回日本生化学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2010-12-08
• [Presentation] 超遠心分析によるT4ファージ尾部基盤ウェッジの逐次的分子集合機構の解明 (2010)
  • Author(s): Moh Lan Yap、三尾和弘、金丸周司、有坂文雄
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 仙台
  • Year and Date: 2010-09-21
• [Presentation] 人工三本鎖βヘリックス蛋白質の設計・発現と会合の制御 (2010)
  • Author(s): 金丸周司、油井孔兵、有坂文雄
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2010-06-17
• [Presentation] 大腸菌O-157と大腸菌CFT073のタイプ6分泌系のVgrG蛋白質の性状解析 (2010)
  • Author(s): 内田一也、金丸周司、有坂文雄
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2010-06-17
• [Presentation] In vitro-assembled wedges of phage T4 spontaneously associate to form hub-less baseplate-like structure (2009)
  • Author(s): Yap Moh Lan・三尾和弘・Petr G. Leiman・門崎泰憲・金丸周司・有坂文雄
  • Organizer: 特定領域研究「生体超分子構造」第6回シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2009-12-01
• [Presentation] 大腸菌タイプVI分泌系のVgrGタンパク質の可溶向上の試み (2009)
  • Author(s): 内田一也・金丸周司・有坂文雄
  • Organizer: 特定領域研究「生体超分子構造」第6回シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2009-12-01
• [Presentation] T4ファージ尾部ウェッジ複合体形成反応測定のための変異体gp11の作製 (2009)
  • Author(s): 竹口誠也・金丸周司・有坂文雄
  • Organizer: 特定領域研究「生体超分子構造」第6回シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2009-12-01
• [Presentation] T4ファージgp34N末端決失変異体の大量発現系の作製と性情解析 (2009)
  • Author(s): 名村実公賢・金丸周司・有坂文雄
  • Organizer: 特定領域研究「生体超分子構造」第6回シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2009-12-01
• [Presentation] 人工3本鎖β-ヘリックス蛋白質の改変 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 特定領域研究「生体超分子構造」第6回シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2009-12-01
• [Presentation] In vitro-assembled wedges of phage T4 spontaneously associate to formhub-less baseplate-like structure (2009)
  • Author(s): Yap Moh Lan・三尾和弘・Petr G.Leiman・門崎泰憲・金丸周司・有坂文雄
  • Organizer: 特定領域研究「生体超分子構造」第6回シンポジウム
  • Place of Presentation: 大阪
  • Year and Date: 2009-12-01
• [Presentation] Baseplate Wedge Assembly of Bacteriophage T4 in vitro (2009)
  • Author(s): Yap Moh Lan・金丸周司・有坂文雄
  • Organizer: 日本生物物理学会第47回年会
  • Place of Presentation: 淡路島
  • Year and Date: 2009-10-29
• [Presentation] 人工3本鎖β-ヘリックス蛋白質の効率的生産と会合抑制 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 日本生化学会年会
  • Place of Presentation: 神戸
  • Year and Date: 2009-10-24
• [Presentation] Spackle Protein and Tail Lysozyme(gp5) of Bacteriophage T4 (2009)
  • Author(s): Shuji Kanamaru, Mai Nemoto, Mako Okuda and Fumio Arisaka
  • Organizer: The 21st Biannual Phage/Virus Assembly Meeting
  • Place of Presentation: フランス・アヌシー
  • Year and Date: 2009-09-25
• [Presentation] In vitro Assembled Wedge of Phage T4 Spontaneously Formed Baseplate-like Structure (2009)
  • Author(s): Moh Lan Yap, Yasunori Monzaki, Kazuhiro Mio, Petr Leiman, Shuji Kanamaru, and Fumio Arisaka
  • Organizer: The 21st Biannual Phage/Virus Assembly Meeting
  • Place of Presentation: フランス・アヌシー
  • Year and Date: 2009-09-25
• [Presentation] Spackle Protein and Tail Lysozyme(gp5)of Bacteriophage T4 (2009)
  • Author(s): Shuji Kanamaru, Mai Nemoto, Mako Okuda, Fumio Arisaka
  • Organizer: The 21st Biannual Phage/Virus Assembly Meeting
  • Place of Presentation: フランス・アヌシー
  • Year and Date: 2009-09-25
• [Presentation] T4ファージ溶菌阻止関連蛋白質gp61.3の結晶化 (2009)
  • Author(s): 奥田真子・根本舞・金丸周司有坂文雄
  • Organizer: 特定領域研究「第5回ワークショップ」
  • Place of Presentation: 湘南国際村
  • Year and Date: 2009-07-28
• [Presentation] 大腸菌0-157のタイプVI分泌系のVgrGタンパク質の性状解析 (2009)
  • Author(s): 内田一也・金丸周司・有坂文雄
  • Organizer: 特定領域研究「第5回ワークショップ」
  • Place of Presentation: 湘南国際村
  • Year and Date: 2009-07-28
• [Presentation] In vitro-Assembled Wedges of Phage T4 Form a Star-shaped Baseplate (2009)
  • Author(s): Moh Lan Yap, Yasunori Monzaki, Kazuhiro Mio, Petr G Leiman, Shuji Kanamaru, and Fumio Arisaka
  • Organizer: 特定領域研究「第5回ワークショップ」
  • Place of Presentation: 湘南国際村
  • Year and Date: 2009-07-27
• [Presentation] 人工三本鎖β-ヘリックス蛋白質の会合抑制 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 特定領域研究「第5回ワークショップ」
  • Place of Presentation: 湘南国際村
  • Year and Date: 2009-07-27
• [Presentation] T4ファージ溶菌阻止関連蛋白質gp61. 3の結晶化 (2009)
  • Author(s): 奥田真子・根本舞・金丸周司,有坂文雄
  • Organizer: 特定領域研究「第5回ワークショップ」
  • Place of Presentation: 湘南国際村
  • Year and Date: 2009-07-27
• [Presentation] 大腸菌O-157のタイプVI分泌系のVgrGタンパク質の性状解析内田一也 (2009)
  • Author(s): 金丸周司・有坂文雄
  • Organizer: 特定領域研究「第5回ワークショップ」
  • Place of Presentation: 湘南国際村
  • Year and Date: 2009-07-27
• [Presentation] The baseplate wedge assembly pathway of phage T4 in vitro (2009)
  • Author(s): Yap Moh Lan・中尾朋子・長尾達也・門崎泰憲・三尾和弘・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-21
• [Presentation] 人工3本鎖β-Helix蛋白質の効率的生産と会合抑制 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-21
• [Presentation] T4ファージの溶菌阻止に関与するSp蛋白質の構造と機能 (2009)
  • Author(s): 根本舞・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-21
• [Presentation] 人工3本鎖β-Helix 蛋白質の効率的生産と会合抑制 (2009)
  • Author(s): 油井孔兵・寺内允・金丸周司・有坂文雄
  • Organizer: 第9回蛋白質科学会年会
  • Place of Presentation: 熊本
  • Year and Date: 2009-05-21