Three-dimensional structure analysis of bacterial pheromone receptor and transporter membrane protein and its application to the design of novel bacteriostatic agents

• Project/Area Number: 16087203
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: The University of Tokyo
• Principal Investigator: NAGATA Koji The University of Tokyo, 大学院・農学生命科学研究科, 准教授 (30280788)
• Co-Investigator(Kenkyū-buntansha): NAKAYAMA Jiro 九州大学, 大学院・農学研究院, 准教授 (40217930)
• Project Period (FY): 2004 – 2009
• Project Status: Completed (Fiscal Year 2009)
• Budget Amount: ¥68,200,000 (Direct Cost: ¥68,200,000); Fiscal Year 2009: ¥8,000,000 (Direct Cost: ¥8,000,000); Fiscal Year 2008: ¥8,000,000 (Direct Cost: ¥8,000,000); Fiscal Year 2007: ¥14,100,000 (Direct Cost: ¥14,100,000); Fiscal Year 2006: ¥14,100,000 (Direct Cost: ¥14,100,000); Fiscal Year 2005: ¥16,000,000 (Direct Cost: ¥16,000,000); Fiscal Year 2004: ¥8,000,000 (Direct Cost: ¥8,000,000)
• Keywords: quorum sensing / Enterococcus faecalis / histidine kinase / peptide pheromone / membrane protein / signal transduction / two component system / response regulator

Research Abstract

The gelatinase production by Enterococcus faecalis is regulated by the cyclic peptide pheromone, GBAP. We determined the tertiary structure of GBAP and identified the important residues for its pheromone activity. We also developed GBAP antagonists by Ala mutations based on the structural information. We expressed in Escherichia coli, purified and crystallized recombinant FsrC, the GBAP receptor membrane protein. A crystal of FsrC-GBAP complex diffracted X-rays to 5.5-Aresolution.

Research Products

• [Journal Article] Biosynthesis of the thiolactone derivative of Enterococcus faecalis gelatinase- biosynthesis activating pheromone by using the Mycobacterium xenopi GyrA mini-intein (2010)
  • Author(s): Yamanaka, Y., Hayakawa, K., Katayama, H., Nishiguchi, K., Sonomoto, K., Nakayama, J., Nagata, K., Tanokura, M
  • Journal Title: Peptide Science 2009 (Okamoto K ed. ) Pages: 171-172
  • Peer Reviewed
• [Journal Article] Biosynthesis of the thiolactone derivative of Enterococcus faecalis gelatinase-biosynthesis activating pheromone by using the Mycobacterium xenopi GyrA mini-intein (2010)
  • Author(s): Yamanaka Y, Hayakawa K, Katayama H, Nishiguchi K, Sonomoto K, Nakayama J, Nagata K., Tanokura M
  • Journal Title: Peptide Science 2009(Okamoto K ed.)(The Japanese Peptide Society) Pages: 171-172
  • Peer Reviewed
• [Journal Article] Structure-activity relationship of gelatinase biosynthesis-activating pheromone of Enterococcus faecalis (2009)
  • Author(s): Nishiguchi, K., Nagata, K., Tanokura, M., Sonomoto, K., Nakayama, J
  • Journal Title: J. Bacteriol 191 Pages: 641-650
  • Peer Reviewed
• [Journal Article] Structure-activity relationship of gelatinase biosynthesis-activating pheromone of Enterococcus faecalis (2009)
  • Author(s): Nishiguchi, K., Nagata, K. Tanokura, M. , Sonomoto, K. and Nakayama. J.
  • Journal Title: J. Bacteriol. 191 Pages: 641-650
  • Peer Reviewed
• [Journal Article] Crystal structure of calcium-bound human SI00A13 at pH 7.5 at 1.8-A resolution (2008)
  • Author(s): Imai, F. L., Nagata, K., Yo nezawa, N., Nakano, M. and Tanokura, M.
  • Journal Title: Acta Crystallogr F64 Pages: 70-76
  • Peer Reviewed
• [Journal Article] A unique catalytic triad revealed by the crystal structure of APE0912 , a short-chain dehydrogenase/reductase family protein from Aeropyrum pernix Kl (2008)
  • Author(s): Yamamura, A., Ichimura, T., Mimoto, F., Ohtsuka, J., Miyazono, K. , Okai, M., Kamo, M., Lee, W .-C., Nagata, K. and Tanokura, M.
  • Journal Title: Proteins 70 Pages: 1640-1645
  • Peer Reviewed
• [Journal Article] Crystal structure of the proline iminopeptidase-related protein TTHA1 809 from Thermus thermophilus HB8 (2008)
  • Author(s): Okai, M., Miyauchi, Y. , Lee, W. C., Yumoto, F., Nagata, K. and Tanokura, M.
  • Journal Title: Proteins 70 Pages: 1646-1649
  • Peer Reviewed
• [Journal Article] Spectroscopic and ITC study of the conformational change upon Ca"-bin ding in TnC C-lobe and TnI peptide complex from Akazara scallop striated muscle (2008)
  • Author(s): Yumoto, F., Tanaka, H., Nagata, K., Miyauchi, Y., Miyakawa, T. Ojima, T. and Tanokura, M.
  • Journal Title: Biocbem. Biophys. Res. Commun. 369 Pages: 109-114
  • Peer Reviewed
• [Journal Article] Synergistic activation of Arabidopsis NADPH oxidase AtrbohD by Ca^<2+> and phosphorylation (2008)
  • Author(s): Ogasawara, Y., Kaya, H., Hiraoka, G., Yumoto, F., Kimura, S., Kadota, Y. , Hishinuma, H., Senzaki, E., Yamagoe, S., Nagata, K Nara, M., Suzuki, K. , Tanokura, M. and Kuchitsu, K.
  • Journal Title: J. Biol. Chem. 283 Pages: 8885-8892
  • Peer Reviewed
• [Journal Article] Crystal structure of TTHA1429, a novel metallo-O-lactamase superfamily Protein from Thermus thermophilus HB8 (2008)
  • Author(s): Yamamura, A. , Ohtsuka, J., Kubota, K., Agari, Y., Ebihara, A., Nakagawa, N. Nagata, K. and T anokura. M.
  • Journal Title: Proteins 73 Pages: 1053-1057
  • Peer Reviewed
• [Journal Article] Crystal structure of TTHA0303 (TT2238), a four-helix bundle protein with an exposed histidine triad from Thermus thermophilus HB8 at 2.0 Å (2008)
  • Author(s): Nagata, K., Ohtsuka, J., Takaha shi, M., Asano, A., Iino, H., Ebihara, A. and Tanokura, M.
  • Journal Title: Proteins 70 Pages: 1103-1107
  • Peer Reviewed
• [Journal Article] Siamycin attenuates fsr quorum sensing mediated by gelatinase biosynthesis-activating pheromone in Enterococcus faecalis (2007)
  • Author(s): Nakayama, J., Tanaka, E., Kariyama, R., Nagata, K., Nishiguchi, K., Mitsuhata, R., Uemura, Y., Tanokura, M., Kumon, H., Sonomoto, K
  • Journal Title: J. Bacteriol 189 Pages: 1358-1365
  • Peer Reviewed
• [Journal Article] Homodimeric structure and double-stranded RNA cleavage activity of the C-terminal RNase III domain of human Dicer (2007)
  • Author(s): Takeshita, D., Zenno, S., Lee, W. C., Nagata, K., Saigo, K. and Tanokura, M.
  • Journal Title: J. Mol. Biol. 374 Pages: 106-120
  • Peer Reviewed
• [Journal Article] Reversible and irreversible coiled coils in the stalk domain of ncd motor protein (2007)
  • Author(s): Makino, T., Morii, H., Shimizu, T., Arisaka, F., Kato, Y., Nagata, K. and Tanokura, M.
  • Journal Title: Biochemistry 46 Pages: 9523-9532
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray analysis of the Ca2+-bound C-terminal lobe of troponin C in complex with a troponin I-derived peptide fragment from Akazara scallop (2007)
  • Author(s): Yumoto, F., Nagata, K., Miyauchi, Y., Ojima, T., Tanaka, H., Nishita, K., Ohtsuki, I. and Tanokura, M.
  • Journal Title: Acta Crystallogr. F63 Pages: 535-537
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray analysis of PH1010 from Pyrococcus horikoshii OT3, a member of the archaeal DUF54 famil of proteins. (2007)
  • Author(s): Shirokane, M., Sawano, Y., Miyazono, K., Nagata K. and Tanokura, M.
  • Journal Title: Acta Crystallogr. F63 Pages: 532-534
  • Peer Reviewed
• [Journal Article] Novel protein fold discovered in the PabI family of restriction enzymes. (2007)
  • Author(s): Miyazono, K., Watanabe, M., Kosinski, J., Ishikawa, K., Kamo, M., Sawasaki, T., Nagata, K., Bujnicki, J. M., Endo, Y., Tanokura, M. and Kobayashi, I.
  • Journal Title: Nucl. Acids Res. 35 Pages: 1908-1918
  • Peer Reviewed
• [Journal Article] Crystal structure of thioredoxin domain of ST2123 from thermophilic archaea Sulfolobus tokodaii strain7 (2007)
  • Author(s): Ming, H., Kato, Y., Miyazono, K., Ito, K., Kamo, M., Nagata, K. and Tanokura, M.
  • Journal Title: Proteins 69 Pages: 204-208
  • Peer Reviewed
• [Journal Article] Crystal structure of Dim2p, a pre-ribosomal RNA processing factor, from Pyrococcus horikoshii OT3 at 2.30 Å (2007)
  • Author(s): Jia, M. Z., Otsuka, J., Lee, W. C., Nagata, K. and Tanokura, M
  • Journal Title: Proteins 69 Pages: 428-432
  • Peer Reviewed
• [Journal Article] Solution structure and binding specificity of FBPII/HYPA WW domain as Group-II/III. (2006)
  • Author(s): Kato, Y., Hino, Y., Nagata, K., Tanokura, M.
  • Journal Title: Proteins 63 Pages: 227-234
• [Journal Article] Crystallization and preliminary X-ray analysis of the C-terminal RNase III domain of human Dicer. (2006)
  • Author(s): Takeshita, D., Zenno, S., Lee, W.C., Nagata, K., Saigo, K., Tanokura, M.
  • Journal Title: Acta Crystallogr. F62 Pages: 402-404
• [Journal Article] Crystal structures of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7 in its three states [NAD (P)^+-free, NAD^+-bound, and NADP^+-bound]. (2006)
  • Author(s): Okai, M., Kudo, N., Lee, W.C., Kamo, M., Nagata, K., Tanokura, M.
  • Journal Title: Biochemistry 45 Pages: 5103-5110
• [Journal Article] Crystallization and preliminary X-ray analysis of CTP : phosphoethanolamine cytidylyltransferase (ECT) from Saccharomyces cerevisiae. (2006)
  • Author(s): Ohtsuka, J., Nagata, K., Lee, W.C., Ono, Y., Fukuda, R., Ohta, A., Tanokura, M.
  • Journal Title: Acta Crystallogr. F62 Pages: 1003-1005
• [Journal Article] Crystallization and preliminary X-ray analysis of human S100A13. (2006)
  • Author(s): Imai, F.L., Nagata, K., Yonezawa, N., Yu, J., Ito, E., Kanai, S., Tanokura, M., Nakano, M.
  • Journal Title: Acta Crystallogr. F62 Pages: 1144-1146
• [Journal Article] Siamycin attenuates fsr quorum sensing mediated by gelatinase biosynthesis-activating pheromone in Enterococcus faecalis. (2006)
  • Author(s): Nakayama, J., Tanaka, E., Kariyama, R., Nagata, K.(5名), Sonomoto, K.
  • Journal Title: J. Bacteriol. 189 Pages: 1358-1365
• [Journal Article] Crystal Structure of the YjgF/YER057c/UK114 Family Protein from the hyperthermophilic archaeon Sulfolobus tokodaii (2006)
  • Author(s): Miyakawa, T., (5名), Nagata, K., Tanokura, M.
  • Journal Title: Proteins 62 Pages: 557-561
• [Journal Article] Crystallization and preliminary X-ray analysis of PH1566, aputative ribosomal RNA processing factor from the hyperthermophilic archaemon Pyrococcus horikoshii OT3. (2006)
  • Author(s): Jia, M.Z., Ohtsuka, J., Lee, W.C., Nagata, K., Tanokura, M.
  • Journal Title: Acta Crystailographica Section F : Structural biology and Crystallization communications 62 Pages: 47-48
• [Journal Article] Crystal structure of monomeric sarcosine oxidase from Bacillus sp. NS-129 reveals multiple conformations at the active-site loop. (2005)
  • Author(s): Nagata, K.et al.(計11名)
  • Journal Title: Proceedings of the Japan Academy, Ser.B 81 Pages: 220-224
  • NAID: 130000093800
• [Journal Article] Crystal structure of the short-chain flavin reductase HpaC from Sulfolobus tokodaii strain 7. (2005)
  • Author(s): Okai, M., Kudo, N., Nagata, K., Lee, W.C., Kamo, M., Tanokura, M.
  • Journal Title: Proceedings of the Japan Academy, Ser.B 81 Pages: 229-232
  • NAID: 130000093802
• [Journal Article] Crystallization and preliminary X-ray analysis of the YjgF/YER057c/UK114-family protein ST0811 from Sulfolobus tokodaii strain 7. (2005)
  • Author(s): Miyakawa, T., (5名), Nagata, K., Tanokura, M.
  • Journal Title: Acta Crystallographica Section F : Structural Biology and Crystallization Communications 61 Pages: 828-830
• [Journal Article] Crystal structure of glutamine amidotransferase from Pyrococcus horikoshii OT3. (2005)
  • Author(s): Maruoka, S., Lee, W.C., Kamo, M., Kudo, N., Nagata, K., Tanokura, M.
  • Journal Title: Proceedings of the Japan Academy, Ser.B 81 Pages: 459-462
  • NAID: 130000093819
• [Journal Article] Preliminary X-ray crystallographic analysis of thermolysin in the presence of 4 M NaCl. (2005)
  • Author(s): Kamo, M., Inouye, K., Nagata, K., Tanokura, M.
  • Journal Title: Acta Crystallographica Section D : Biological Crystallography 61(印刷中)
• [Journal Article] Crystallization and preliminary X-ray analysis of carboxypeptidase 1 from Thermus thermophilus. (2004)
  • Author(s): Nagata, K.et al.(計7名)
  • Journal Title: Acta Crystallographica Section D : Biological Crystallography 60 Pages: 1445-1446
• [Presentation] 腸球菌のクオーラムセンシング自己誘導因子GBAPのチオラクトン誘導体の生合成とその受容体FsrCとの相互作用解析 (2010)
  • Author(s): 山中陽介、片山秀和、山村昭裕、堀田彰一朗、早川江、西口賢三、佐藤まみ、園元謙二、中山二郎、永田宏次、田之倉優
  • Organizer: 日本農芸化学会2010年度(平成22年度)大会
  • Place of Presentation: 東京都目黒区
  • Year and Date: 2010-03-28
• [Presentation] 腸球菌のクオーラムセンシング自己誘導因子GBAPのチオラクトン誘導体の生合成とその受容体FsrCとの相互作用解析 (2010)
  • Author(s): 山中陽介、片山秀和、山村昭裕、堀田彰一朗、早川江、西口賢三、佐藤まみ、園元謙二、中山二郎、永田宏次、田之倉優
  • Organizer: 日本農芸化学会2010年度(平成22年度)大会
  • Place of Presentation: 目黒区(東京都)
• [Presentation] 腸球菌のクオーラムセンシング自己誘導因子GBAPのチオラクトン誘導体のミニインテイン融合タンパク質システムを利用した生合成 (2009)
  • Author(s): 山中陽介、早川江、片山秀和、山村昭裕、堀田彰一朗、西口質三、園元謙二、中山二郎、永田宏次、田之倉優
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 神奈川県横浜市
  • Year and Date: 2009-12-12
• [Presentation] Biosynthesis of the thiolactone derivative of Enterococcus faecalis gelatinase-biosynthesis activating pheromone by using the Mycobacterium xenopi GyrA mini-intein (2009)
  • Author(s): 山中陽介, 早川江, 片山秀和, 西口質三, 園元謙二, 中山二郎, 永田宏次, 田之倉優
  • Organizer: 第46回ペプチド討論会
  • Place of Presentation: 福岡県北九州市
  • Year and Date: 2009-11-04
• [Presentation] 腸球菌のクオーラムセンシングを制御する環状ペプチドフェロモン(GBAP)の構造および機能解析 (2009)
  • Author(s): 西口賢三、永田宏次、佐藤まみ、田之倉優、園元謙二、中山二郎
  • Organizer: 日本農芸化学会2009年度大会
  • Place of Presentation: マリンメッセ福岡(福岡県)
  • Year and Date: 2009-03-29
• [Presentation] グラム陽性菌のクオラムセンシング阻害剤の開発と展望 (2009)
  • Author(s): 中山二郎、西口賢三、永田宏次、田中笑美、上村結美、吉村憲人、五十嵐康弘、園元謙二
  • Organizer: 日本農芸化学会2009年度大会
  • Place of Presentation: マリンメッセ福岡(福岡県)
  • Year and Date: 2009-03-28
• [Presentation] 腸球菌のクオーラムセンシング自己誘導因子GBAPのチオラクトン誘導体のミニインテイン融合タンパク質システムを利用した生合成 (2009)
  • Author(s): 山中陽介、早川江、片山秀和、山村昭裕、堀田彰一朗、西口賢三、園元謙二、中山二郎、永田宏次、田之倉優
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: 横浜市(神奈川県)
• [Presentation] Biosynthesis of the thiolactone derivative of Enterococcus faecalis gelatinase- biosynthesis activating pheromone by using the Mycobacterium xenopi GyrA mini-intein (2009)
  • Author(s): Yamanaka, Y., Hayakawa, K., Katayama, H., Nishiguchi, K., Sonomoto, K., Nakayama, J., Nagata, K., Tanokura, M
  • Organizer: 第46回ペプチド討論会
  • Place of Presentation: 北九州市(福岡県)
• [Presentation] 腸球菌のクオーラムセンシングを制御する環状ペプチドフェロモン(GBAP)の構造および機能解析 (2009)
  • Author(s): 西口賢三、永田宏次、佐藤まみ、田之倉優、園元謙二、中山二郎
  • Organizer: 日本農芸化学会2009年度大会
  • Place of Presentation: 福岡市(福岡県)
• [Presentation] グラム陽性菌のクオラムセンシング阻害剤の開発と展望 (2009)
  • Author(s): 中山二郎、西口賢三、永田宏次、田中笑美、上村結美、吉村憲人、五十嵐康弘、園元謙二
  • Organizer: 本農芸化学会2009年度大会
  • Place of Presentation: 福岡市(福岡県)
• [Presentation] 腸球菌のクォルモンGBAPと受容体FsrCの相互作用解析 (2008)
  • Author(s): 永田宏次、西口賢三、亀田泰広、山村昭裕、中山二郎、園元謙二、田之倉優
  • Organizer: 文部科学省特定領域研究「生体超分子構造」第5回公開シンポジウム
  • Place of Presentation: つくば国際会議場(茨城県)
  • Year and Date: 2008-12-18
• [Presentation] Structure-Activity Relationship of Gelatinase Biosynthesis-Activating Pheromone from the Gram Positive Bacterium Enterococcus faecalis (2008)
  • Author(s): Koji Nagata, Kenzo Nishiguchi, Masaru Tanokura, Kenji Sonomoto and Jiro Nakayama
  • Organizer: 第45回ペプチド討論会
  • Place of Presentation: タワーホール船堀(東京都)
  • Year and Date: 2008-10-30
• [Presentation] 腸球菌のクオーラムセンシングに関わるタンパク質の構造・機能解析 (2008)
  • Author(s): 永田宏次、山村昭裕、堀田彰一朗、山中陽介、秋野隆文、西口賢三、中山二郎、園元謙二、田之倉優
  • Organizer: 文部科学省特定領域研究「生体超分子構造」第6回公開シンポジウム
  • Place of Presentation: 吹田市(大阪府)
• [Presentation] 腸球菌のクォルモンGBAPと受容体FsrCの相互作用解析 (2008)
  • Author(s): 永田宏次、西口賢三、亀田泰広、山村昭裕、中山二郎、園元謙二、田之倉優
  • Organizer: 文部科学省特定領域研究「生体超分子構造」第5回公開シンポジウム
  • Place of Presentation: つくば市(茨城県)
• [Presentation] 腸球菌のクオーラムセンシングに関わるタンパク質の構造・機能解析 (2007)
  • Author(s): 永田宏次、高橋美穂子、浅野敦子、山本真智子、筒井志穂、亀田泰広、西口賢三、中山二郎、園元謙二、田之倉優
  • Organizer: 文部科学省特定領域研究「生体超分子構造」第4回公開シンポジウム
  • Place of Presentation: 千里ライフサイエンスセンター(大阪府)
  • Year and Date: 2007-12-18
• [Presentation] 腸球菌のクオーラムセンシングに関わるタンパク質の構造・機能解析 (2007)
  • Author(s): 永田宏次、高橋美穂子、浅野敦子、山本真智子、筒井志穂、亀田泰広、西口賢三、中山二郎、園元謙二、田之倉優
  • Organizer: 文部科学省特定領域研究「生体超分子構造」第4回公開シンポジウム
  • Place of Presentation: 吹田市(大阪府)
• [Presentation] 腸球菌のペプチドフェロモンGBAPとその受容体膜タンパク質FsrCの構造解析 (2007)
  • Author(s): 永田宏次, 高橋美穂子, 浅野敦子, 筒井志穂, 山田邦永, 西口賢三, 中山二郎, 園元謙二, 田之倉優
  • Organizer: 日本農芸化学会
  • Place of Presentation: 世田谷区(東京都)
• [Presentation] 腸球菌のクオーラムセンシングを制御する環状ペプチドの構造活性相関研究 (2006)
  • Author(s): 西口賢三, 中山二郎, 永田宏次, 田之倉優, 園元謙二
  • Organizer: 文部科学省特定領域研究「生体超分子の構造形成と機能制御の原子機構」第3回公開シンポジウム
  • Place of Presentation: つくば市(茨城県)
• [Presentation] 腸球菌のクオーラムセンシングに関わるタンパク質の構造解析 (2006)
  • Author(s): 永田宏次, 高橋美穂子, 浅野敦子, 筒井志穂, 山田邦永, 西口賢三, 中山二郎, 園元謙二, 田之倉優
  • Organizer: 文部科学省特定領域研究「生体超分子の構造形成と機能制御の原子機構」第3回公開シンポジウム
  • Place of Presentation: つくば市(茨城県)
• [Presentation] 腸球菌fsr制御系を標的としたクォーラムセンシング阻害剤開発に関する研究 (2005)
  • Author(s): 中山二郎, 永田宏次, 田中笑美, 西口賢三, 陳晟敏, 小山望, 田之倉優, 園元謙二
  • Organizer: 文部科学省特定領域研究「生体超分子の構造形成と機能制御の原子機構」第2回公開シンポジウム
  • Place of Presentation: 金沢市(石川県)
• [Presentation] 腸球菌のペプチドフェロモン受容体膜タンパク質FsrCの大腸菌での発現、精製、機能解析 (2005)
  • Author(s): 永田宏次, 筒井志穂, 中山二郎, 園元謙二, 田之倉優
  • Organizer: 結晶化、文部科学省特定領域研究「生体超分子の構造形成と機能制御の原子機構」第2回公開シンポジウム
  • Place of Presentation: 金沢市(石川県)
• [Presentation] 腸球菌のペプチドフェロモン受容体膜タンパク質FsrCの大腸菌での発現、精製、構造・機能解析 (2005)
  • Author(s): 永田宏次、筒井志穂、中山二郎、園元謙二、田之倉優
  • Organizer: 第5回日本蛋白質科学会年会
  • Place of Presentation: 福岡市(福岡県)