Neutron structure analysis of human PGD synthase for elucidation of the reaction mechanism activated by metal ions

2012 Fiscal Year Final Research Report

• Project/Area Number: 22550152
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Chemistry related to living body
• Research Institution: Osaka University
• Principal Investigator: INOUE Tsuyoshi 大阪大学, 大学院・工学研究科, 教授 (20263204)
• Co-Investigator(Kenkyū-buntansha): MATSUMURA Hiroyoshi 大阪大学, 大学院・工学研究科, 准教授 (30324809) ; MIZOHATA Eiichi 大阪大学, 大学院・工学研究科, 助教 (90571183)
• Project Period (FY): 2010 – 2012
• Keywords: 中性子線解析 / 金属イオン / 酵素活性化機構

Research Abstract

Prostaglandin D_2(PGD_2) is an allergic and inflammatory mediator produced by hematopoietic PGDS (H-PGDS) in the presence of glutathione (GSH). Previously, we found that Ca^2+and Mg^2+activated the enzyme activity and uncovered the activation mechanism by the X-ray crystal structures of the Ca^2+- and Mg^2+-bound forms of human H-PGDS at high resolution. In this study, we performed the crystallization of H-PGDS to reveal the protonation state by neutron diffraction and obtained the crystals with maximum size of 0.5 mm^3with high quality.

Research Products

• [Journal Article] Human hematopoietic prostaglandin D synthase inhibitor complex structures (2012)
  • Author(s): Y. Kado, Y. Okano, N. Okazaki, K. Aritake, N. Uodome, H. Matsumura, Y. Urade & T. Inoue
  • Journal Title: J. Biochem Volume: 151 Pages: 447-455
• [Journal Article] Three-dimensional, non-invasive, cross-sectional imaging of protein crystals using ultrahigh resolution optical coherence tomography (2012)
  • Author(s): N. Nishizawa, S. Ishida, M. Hirose, S. Sugiyama, T. Inoue, Y. Mori, K. Itoh & H. Matsumura*
  • Journal Title: Biomed. Opt. Express Volume: 3 Pages: 735-740
• [Journal Article] Growth of protein crystals in hydrogels prevents osmotic shock (2012)
  • Author(s): S. Sugiyama, M. Maruyama, G. Sazaki, M. Hirose, H. Adachi, K. Takano, S. Murakami, T. Inoue, Y. Mori & H. Matsumura*
  • Journal Title: J. Am. Chem. Soc. Volume: 134 Pages: 5786-5789
• [Journal Article] Crystal structure of the superfamily 1 helicase from Tomato mosaic virus (2012)
  • Author(s): M. Nishikiori, S. Sugiyama, H. Xiang, M. Niiyama, K. Ishibashi, T. Inoue, M. Ishikawa, H. Matsumura & E. Katoh*
  • Journal Title: J. Virol. Volume: 86 Pages: 7565-7576
• [Journal Article] Effects of a forced solution flow on the step advancement on {110} faces of tetragonal lysozyme crystals: direct visualization of individual steps under a forced solution flow (2012)
  • Author(s): M. Maruyama, K. Hisato, G. Sazaki, S. Maki, Y. Takahashi, H. Yoshikawa, S. Sugiyama, H. Adachi, K. Takano, H. Matsumura, T. Inoue, S. Murakami & Y. Mori
  • Journal Title: Cryst. Growth Des. Volume: 12 Pages: 2856-2863
• [Journal Article] The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase (2012)
  • Author(s): Y. Takashima, E. Mizohata, S. R. Krungkrai, Y. Fukunishi, T. Kinoshita, T. Sakata, H. Matsumura, J. Krungkrai, T. Horii & T. Inoue
  • Journal Title: J. Biochem. Volume: 152 Pages: 133-138
• [Journal Article] Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p and its functional implications (2012)
  • Author(s): H. Matsumura*, N. Kusaka, T. Nakamura, N. Tanaka, K. Sagegami, K. Uegaki, T. Inoue & Y. Mukai
  • Journal Title: J. Biol. Chem. Volume: 287 Pages: 26528-26538
• [Journal Article] Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate (2012)
  • Author(s): H. Matsumura, E. Mizohata, H. Ishida, A. Kogami, T. Ueno, A. Makino, T. Inoue, A. Yokota, T. Mae & Y. Kai*
  • Journal Title: J. Mol. Biol. Volume: 422 Pages: 75-86
• [Journal Article] Spatially precise, soft microseeding of single protein crystals by femtosecond laser ablation (2012)
  • Author(s): H. Yoshikawa, Y. Hosokawa, R. Murai, G. Sazaki, T. Kitatani, H. Adachi, T. Inoue, H. Matsumura, K. Takano, S. Murakami, S. Nakabayashi, Y. Mori & H. Matsumura
  • Journal Title: Cryst. Growth Des. Volume: 12 Pages: 4334-4339
• [Journal Article] Structural insight into the stereoselective production of PGF_2αby Old Yellow Enzyme from Trypanosoma cruzi (2011)
  • Author(s): N. Okamoto, K. Yamaguchi, E. Mizohata, K. Tokuoka, N. Uchiyama, S. Sugiyama, H. Matsumura, K. Inaka, Y. Urade, T. Inoue
  • Journal Title: J. of Biochemistry Volume: 150 Pages: 563-568
• [Journal Article] Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F_2αsynthase, AKR1B3 (2011)
  • Author(s): Y. Takashima, S. Hatanaka, E. Mizohata, N. Nagata, Y. Fukunishi, H. Matsumura, Y. Urade, T. Inoue
  • Journal Title: Acta Cryst. Volume: F67 Pages: 1630-1632
• [Presentation] Atomic resolution structure of copper-containing nitrite reductase provides insights into common properties of type 2 copper-containing enzymes (2012)
  • Author(s): Y. Fukuda, T. Tamada, H. Takami, T. Inoue, M. Nojiri
  • Organizer: Asian Crystallographic Association (AsCA) 2012
  • Place of Presentation: Adelaide (Australia)
  • Year and Date: 20121202-05
• [Presentation] Structural basis enzymes in the pyrimidine biosynthetic pathway of human malaria parasite Plasmodium falciparumfor in silicodrug design (2011)
  • Author(s): Y. Takashima, E. Mizohata, K. Tokuoka, Y. Kusakari, T. Uchida, S. R. Krungkrai, H. Matsumura, J. Krungkrai, T. Horii, T. Inoue
  • Organizer: International Union of Crystallography
  • Place of Presentation: Madrid(Spain)
  • Year and Date: 20110822-30
• [Presentation] Novel Approach for Growth of High-Quality and Large Protein Crystals (2010)
  • Author(s): H. Matsumura, K. Kakinouchi, N. Shimizu, S. Sugiyama, Y. Takahashi, M. Maruyama, R. Murai, H. Adachi, K. Takano, S. Murakami, T. Inoue, Y. Mori
  • Organizer: 3th International Conference on the Crystallization of Biological Macromolecules
  • Place of Presentation: Dublin(Ireland)
  • Year and Date: 20100912-16
• [Presentation] Protein Crystallization in Agarose Gel with High Strength (2010)
  • Author(s): S. Sugiyama, M. Hirose, R. Murai, Y. Takahashi, M. Maruyama, G. Sazaki, H. Adachi, K. Takano, S. Murakami, T. Inoue, H. Matsumura
  • Organizer: 3th International Conference on the Crystallization of Biological Macromolecules
  • Place of Presentation: Dublin(Ireland)
  • Year and Date: 20100912-16
• [Presentation] Development of the new protein crystallization techniques and application for structural analysis of target Enzymes
  • Author(s): T. Inoue, H. Adachi, K. Takano, H. Matsumura, S. Murakami, Y. Mori
  • Organizer: The 10th KIAS Conference on Protein Structure for structural and Function
  • Place of Presentation: Korea Institute for Advanced Study, Seoul, Korea