Structural basis for protein functional transfer by SUMOylation

2007 Fiscal Year Final Research Report Summary

• Project/Area Number: 18370040
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: Kyoto University
• Principal Investigator: SHIRAKAWA Masahiro Kyoto University, Graduate School of Engineering, Department of Engineering, Professor (00202119)
• Co-Investigator(Kenkyū-buntansha): TENNNO Takeshi
• Project Period (FY): 2006 – 2007
• Keywords: SUMO / protein modification / structure / NMR / DNA methylation

Research Abstract

Human Heat Shock Factor 2 (hHSF2) has been known to be SUMOylated within its DNA binding domain and trimerization domain. Both positive and negative effect on DNA binding activity by SUMOylation had been reported. In order to investigate the mechanism of regulation of DNAbinding activity of hHSF2 by SUMOylation, we analyzed DNA binding activity of the DNA binding domain (DBD) of hHSF2 and observed the effect of SUMOylation. The result indicated that SUMOylation decreases DNA binding activity of hHSF2 DBD. The results of NMR and pulse ESR experiments and model building suggest that the SUMO moiety on SUMO-attached hHSF2 DBD is not fixed, and thus diversely positioned relative to hHSF2 DBD, but the SUMO moiety tend to be in proximity to the putative DNA binding surface of hSF2 DBD. We proposed the attached SUMO stochastically inhibits DNA access.
We have determined NMR structure of complex of SUMO-3 and the SUMO-interacting motif (SIM) of MCAF1. The structure implies the existence of two interfaces, which mediate mainly hydrophobic and electrostatic interactions, respectively. The latter might be involved in the preferential binding to SUMO-2/3 over SUMO-1 by MCAF1 SIM.
We have determined the crystal structure of the SRA domain of UHRF1 in complex with hemi-methylated DNA. In the complex, a methyl base is flipped out, and is inserted into a pocket of SRA. The structure implies that the flip out mechanism is important for methyl base recognition.

Research Products

• [Journal Article] Molecular basis for SUMOylation-dependent regulation of DNA binding activity of Heat Shock Factor 2. (2009)
  • Author(s): Tateishi, Y., Ariyoshi, M., Igaraahi, R., Hara, H., Mizuguchi, K., Seto, A., Nakai, A., Kokubo, T., Tochio, H., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 284 Pages: 2435-2447
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Molecular basis for SUMOylation-dependent regulation of DNA binding activity of Heat Shock Factor 2. (2009)
  • Author(s): Tateishi, Y., Ariyoshi, M., Igarashi, R., Hara, H., Mizuguchi, K, Seto, A., Nakai, A., Kokubo, T., Tochio, H., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 284 Pages: 2435-2447
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the SUMO-interacting motif of MBD1-containing chromatin associated factor 1 (MCAF1) bound to SUMO-3. (2008)
  • Author(s): Sekiyama, N., Ikegami, T., Yamane, T., Ikeguchi, M., Uchimura, Y., Baba, D., Ariyoshi, M., Tochio, H., Saitoh, H., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 283 Pages: 35966-35975
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Hemi-methylated DNA recognition by the SRA protein Np95 via a base flipping mechanism. (2008)
  • Author(s): Arita, K., Ariyoshi, M., Tochio, H., Nakamura, Y., Shirakawa, M.
  • Journal Title: Nature 455 Pages: 818-821
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Kinetic and Thermodynamic evidence for flipping of a methyl-CpG binding domain on methylated DNA. (2008)
  • Author(s): Inomata, K., Ohki, I., Tochio, H., Fujiwara, K., Hiroaki, H., Shirakawa, M.
  • Journal Title: Biochemistry 47 Pages: 3266-3271
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Paramagnetic Relaxation-Based ^<19>F MRI Probe to Detect Protease Activity. (2008)
  • Author(s): Mizukami, S., Takikawa, R., Sugihara, F., Hori, Y., Tochio, H., Waelchli, M., Shirakawa, M., Kikuchi, K.
  • Journal Title: Journal of the American Chemical Society 130 Pages: 794-795
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structure of the SUMO-interacting motif of MBDl-containing chromatin associated factor 1 (MCAF1) bound to SUMO-3. (2008)
  • Author(s): Sekiyama, N., Ikegami, T., Yamane, T., Ikeguchi, M., Uchimura, Y., Baba, D., Ariyoshi, M., Tochio, H., Saitoh, H., Shirakawa, M.
  • Journal Title: Journal of Biological Chemistry 283 Pages: 35966-35975
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Hemi-methylated DNA recognition by the SRA protein Np95 via a base flipping mechanism. (2008)
  • Author(s): Arita, K, Ariyoshi, M., Tochio, H., Nakamura, Y., Shirakawa, M.
  • Journal Title: Nature 455 Pages: 818-821
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Kinetic and Thermodynamic evidence for flipping of a methyl-CpG binding domain on methylated DNA. (2008)
  • Author(s): Inomata, K, Ohki, I., Tochio, H., Fujiwara, K, Hiroaki, H., Shirakawa, M.
  • Journal Title: Biochemistry 47 Pages: 3266-3271
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Paramagnetic Relaxation-Based ^<19>F MRI Probe to Detect Protease Activity (2008)
  • Author(s): Mizukami, S., Takikawa, R., Sugihara, F., Hori, Y., Tochio, H., Waelchli, M., Shirakawa, M., Kikuchi, K.
  • Journal Title: Journal of the American Chemical Society 130 Pages: 794-795
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural Analysis of Pituitary Adenylate Cyclase-Activating polypeptides Bound to Phospholipid embranes by Magic Angle Spinning Solid-State NMR. (2007)
  • Author(s): Komi, N., Okawa, K., Tateishi, Y., Shirakawa, M., Fujiwara, T., Akutsu, H.
  • Journal Title: Biochimica et Biophysica Acta-Biomembranes 1768 Pages: 3001-3011
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Fluoroscopic assessment of protein leakage during Xenopus oocytes in-cell NMR experiment by co-injected EGFP. (2007)
  • Author(s): Sakai, T., Tochio, H., Inomata, K., Sasaki, Y., Tenno, T., Tanaka, T., Kokubo, T., Hiroaki, H., Shirakawa, M.
  • Journal Title: Analytical Biochemistry 371 Pages: 247-249
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies. (2007)
  • Author(s): Maita, N., Aoyagi, H., Osanai, M., Shirakawa, M., Fujiwara, H.
  • Journal Title: Nucleic Acid Research 35 Pages: 3918-3927
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Magnetic resonance-based visualization of gene expression in mammalian cells using a bacterial polyphosphate kinase reporter gene. (2007)
  • Author(s): Ki, S., Sugihara, F., Kasahara, K., Tochio, H., Shirakawa. M., Kokubo, T.
  • Journal Title: Biotecbniques 42 Pages: 209-215
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] LBT/PTD dual tagged vector for purification, cellular protein delivery and visualization in living cells. (2007)
  • Author(s): Goda, N., Tenno, T., Inomata, K., Iwaya, N., Sasaki, Y., Shirakawa M., Hiroaki. H.
  • Journal Title: Biochemica et Biophysica Acta 1773 Pages: 141-146
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Distance determination in human ubiquitin by pulse double electron resonance and double quantum coherence ESR methods. (2007)
  • Author(s): Hara, H., Tenno, T., Shirakawa, M.
  • Journal Title: Journal of Magnetic Resonance 184 Pages: 78-84
  • Description: 「研究成果報告書概要(和文)」より
  • Peer Reviewed
• [Journal Article] Structural Analysis of Pituitary Adenylate Cyclase-Activating Polypeptides Bound to Phospholipid embranes by Magic Angle Spinning Solid-State NMR. (2007)
  • Author(s): Komi, N., Okawa, K, Tateishi, Y., Shirakawa, M., Fujiwara, T., Akutsu, H.
  • Journal Title: Biochimica et Biophysica Acta Biomembranes 1768 Pages: 3001-3011
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Fluoroscopic assessment of protein leakage during Xenopus oocytes in-cell NMR experiment by co-injected EGFP. (2007)
  • Author(s): Sakai, T., Tochio, H., Inomata, K, Sasaki, Y, Tenno, T., Tanaka, T., Kokubo, T., Hiroaki, H., Shirakawa, M.
  • Journal Title: Analytical Biochemistry 371 Pages: 247-249
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Magnetic resonance-based visualization of gene expression in mammalian cells using a bacterial polyphosphate kinase reporter gene. (2007)
  • Author(s): Ki, S., Sugihara, F., Kasahara, K, Tochio, H., Shirakawa. M., Kokubo, T.
  • Journal Title: Biotechniques 42 Pages: 209-215
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] LBT/PTD dual tagged vector for purification, cellular protein delivery and visualization in living cells. (2007)
  • Author(s): Goda, N., Tenno, T., Inomata, K., Iwaya, N., Sasaki, Y., Shirakawa. M., Hiroaki, H.
  • Journal Title: Biochemica et Biophysica Acta 1773 Pages: 141-146
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Distance determination in human ubiquitin by pulse double electron resonance and double quantum coherence ESR methods. (2007)
  • Author(s): Hara, H., Tenno, T., Shirakawa. M.
  • Journal Title: Journal of Magnetic Resonance 184 Pages: 78-84
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] 蛋白質とDNAの化学修飾による機能調節の構造学的基盤 (2007)
  • Author(s): 白川昌宏
  • Organizer: 東洋紡バイオ財団設立25周年記念シンポジウム
  • Place of Presentation: 大阪市
  • Year and Date: 2007-06-01
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] 磁気共鳴法を使った生体高分子複合体の立体構造解析と細胞計測 (2007)
  • Author(s): 白川昌宏
  • Organizer: 日本顕微鏡学会第63回学術講演会
  • Place of Presentation: 新潟市
  • Year and Date: 2007-05-21
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] 生体防御・制御に関わる蛋白質の構造生物学と生体計測 (2007)
  • Author(s): 白川昌宏
  • Organizer: 第2回岐阜小児アレルギー・喘息研究会
  • Place of Presentation: 岐阜市
  • Year and Date: 2007-05-11
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] NMRとMEIを使った細胞内反応の非侵襲計測 (2007)
  • Author(s): 白川昌宏
  • Organizer: 日本化学会
  • Place of Presentation: 関西大学
  • Year and Date: 2007-03-28
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] 磁気共鳴法による細胞内でのたんぱく質の構造と機能の解析手法 (2006)
  • Author(s): 白川昌宏
  • Organizer: 大阪大学蛋白質研究所セミナー「ケミカルバイオロジーの進展と生命科学研究の新たな展開」
  • Place of Presentation: 大阪大学
  • Year and Date: 2006-11-25
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Structural basis for protein modification by modifier proteinas (2006)
  • Author(s): Shirakawa, M.
  • Organizer: Sapporo conference 2006
  • Place of Presentation: 北海道大学
  • Year and Date: 2006-10-30
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Structural basis for protein modification by modifier proteinas (2006)
  • Organizer: Sapporo conference 2006
  • Place of Presentation: Hokkaido Unniversity
  • Year and Date: 2006-10-30
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] In cell NMR of proteins and non-invasive NMR/MRI detection of gene expression in eukarytotic cells (2006)
  • Author(s): Shirakawa, M.
  • Organizer: 4th Taiwan-Japan NME Symposium
  • Place of Presentation: Institute of Biomedical Sciences, Academia Sinica & Hotel Royal Chiao-Hsi, Taiwan
  • Year and Date: 2006-10-15
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] In cell NMR of proteins and non-invasive NMR/MRI detection of gene expression in eukarytotic cells (2006)
  • Organizer: 4th Taiwan-Japan NMR Symposium
  • Place of Presentation: Institute of Biomedical Sciences, Academia Sinica & Hotel Royal Chiao-Hsi, Taiwan
  • Year and Date: 2006-10-15
  • Description: 「研究成果報告書概要(欧文)」より
• [Presentation] ユビキチン様モディファイアー蛋白質の構造生物学 (2006)
  • Author(s): 白川昌宏
  • Organizer: 日本化学会バイオ関連の化学部合同シンポジウム「生命化学の境界領域 : 構造生物学、ナノバイオ、ケミルバイオ」
  • Place of Presentation: 京都大学
  • Year and Date: 2006-09-29
  • Description: 「研究成果報告書概要(和文)」より
• [Presentation] Structure biology of ubiquitination and SUMOylation (2006)
  • Author(s): Shirakawa, M.
  • Organizer: Switzerland-Japan Symposium on Structural Biology 2006
  • Place of Presentation: Brunnen, Switzerland
  • Year and Date: 2006-09-19
  • Description: 「研究成果報告書概要(和文)」より
• [Book] SUMOによるタンパク質修飾生化学79 (2007)
  • Author(s): 磯貝信, 白川昌宏
  • Total Pages: 11
  • Publisher: 日本生化学会
  • Description: 「研究成果報告書概要(和文)」より
• [Book] 5.2.1たんぱく質“実験化学講座第5版日本化学会編8 NMR・ESR" (2006)
  • Author(s): 杤尾豪人, 白川昌宏
  • Total Pages: 18
  • Publisher: 丸善株式会社
  • Description: 「研究成果報告書概要(和文)」より
• [Book] SUMO化によるたんぱく質の機能調節の構造学的基盤 (2006)
  • Author(s): 白川昌宏
  • Total Pages: 5
  • Publisher: 京都大学低温物質科学研究センター誌
  • Description: 「研究成果報告書概要(和文)」より
• [Book] SUMO化によるたんぱく質機能調節の構造的基盤実験医学 (2006)
  • Author(s): 白川昌宏, 馬場大地
  • Total Pages: 7
  • Publisher: 羊土社
  • Description: 「研究成果報告書概要(和文)」より