Crystal structure analysis of LTTR-DNA complex

• Project/Area Number: 18K06098
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Multi-year Fund
• Section: 一般
• Review Section: Basic Section 43020:Structural biochemistry-related
• Research Institution: High Energy Accelerator Research Organization
• Principal Investigator: Senda Miki 大学共同利用機関法人高エネルギー加速器研究機構, 物質構造科学研究所, 特任助教 (10707467)
• Project Period (FY): 2018-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000); Fiscal Year 2020: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2019: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000); Fiscal Year 2018: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
• Keywords: 転写調節因子 / X線結晶構造解析 / タンパク質ーDNA複合体 / 結晶構造 / DNA複合体 / LysRタイプ転写因子 / 転写 / 全長LTTR-DNA複合体のX線結晶構造解析 / LysRタイプ転写調節因子 / LTTR / タンパク質の結晶化

Outline of Final Research Achievements

In order to elucidate the molecular mechanism of transcriptional activation of LysR-type transcription factors (LTTRs), we studied the transcriptional regulator CbnR of 3-chlorobenzoate-degrading bacteria. The crystal structure of the complex consisting of a full-length CbnR tetramer and 55 base pairs of promoter DNA was determined at 3.6 angstrom resolution. This is the first crystal structure of a full-length LTTR in complex with its cognate promoter DNA.

Academic Significance and Societal Importance of the Research Achievements

LysRタイプ転写因子(LTTR)に関する研究は世界中で行われているが、LTTR-DNA複合体の再構成や結晶化が極めて難しいため、LTTRとプロモーターDNAとの構造情報に基づき結合様式を示した例はなかった。LTTRはアミノ酸生合成・芳香族化合物分解・病原性関連因子産生・酸化ストレスへの応答など多くの転写調節に関与しているため、構造情報を示すことができればLTTRがプロモーターDNAを認識する仕組みについてのジェネラルな知見を得ることができる。

Research Products

• [Journal Article] Crystal structure of the full-length LysR-type transcription regulator (2021)
  • Author(s): Giannopoulou EA, Senda M, Koentjoro MP, Adachi N, Ogawa N, Senda T.
  • Journal Title: FEBS J. Volume: － Issue: 15 Pages: 4560-4575
  • DOI: 10.1111/febs.15764
  • Peer Reviewed
• [Journal Article] Macromolecular Crystallography Using Long Wavelength X-ray (2020)
  • Author(s): 松垣直宏, 山田悠介, 引田理英, 平木雅彦, 千田美紀, 千田俊哉
  • Journal Title: Nihon Kessho Gakkaishi Volume: 62 Issue: 1 Pages: 56-61
  • DOI: 10.5940/jcrsj.62.56
  • NAID: 130007806198
  • ISSN: 0369-4585, 1884-5576
  • Year and Date: 2020-02-29
  • Peer Reviewed / Open Access
• [Journal Article] Reversible control of enantioselectivity by the length of ketone substituent in biocatalytic reduction (2019)
  • Author(s): Koesoema, A., Sugiyama, Y., Sriwong, K. T. Xu, Z., Verina, S. Standley, D. M., Senda, M., Senda, T. & Matsuda, T.
  • Journal Title: Applied Microbiology and Biotechnology Volume: 103 Issue: 23-24 Pages: 9529-9541
  • DOI: 10.1007/s00253-019-10206-5
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Structural basis for highly (S)-enantioselective reductase towards aliphatic ketones with only one carbon difference between side chain (2019)
  • Author(s): Koesoema, A., Sugiyama, Y., Xu, Z., Standley, D. M., Senda, M., Senda, T. & Matsuda, T.
  • Journal Title: Applied Microbiology and Biotechnology Volume: 103 Issue: 23-24 Pages: 9543-9553
  • DOI: 10.1007/s00253-019-10093-w
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Crystal Structure of the DNA-binding Domain of the LysR-type Transcriptional Regulator CbnR in Complex with a DNA Fragment of the Recognition-binding Site (2018)
  • Author(s): 千田 美紀, 安達 成彦, 千田 俊哉, Maharani Pertiwi Koentjoro, 小川 直人
  • Journal Title: Nihon Kessho Gakkaishi Volume: 60 Issue: 2-3 Pages: 135-141
  • DOI: 10.5940/jcrsj.60.135
  • NAID: 130007383391
  • ISSN: 0369-4585, 1884-5576
  • Year and Date: 2018-05-31
  • Peer Reviewed / Open Access
• [Journal Article] Structural and computational bases for dramatic skeletal rearrangement in anditomin biosynthesis (2018)
  • Author(s): Nakashima, Y., Mitsuhashi, T., Matsuda, Y., Senda, M., Sato, H., Yamazaki, M., Uchiyama, M., Senda, T. & Abe, I.
  • Journal Title: JACS Volume: 140 Issue: 30 Pages: 9743-9750
  • DOI: 10.1021/jacs.8b06084
  • Peer Reviewed
• [Journal Article] Crystal structure of the DNA-binding domain of the LysR-type transcriptional regulator CbnR in complex with a DNA fragment of the recognition-binding site in the promoter region. (2018)
  • Author(s): Koentjoro MP, Adachi N, Senda M, Ogawa N, Senda T.
  • Journal Title: FEBS J. Volume: 285(5) Issue: 5 Pages: 977-989
  • DOI: 10.1111/febs.14380
  • Peer Reviewed / Open Access
• [Presentation] Comprehensive strategy for quick determination of protein structures. (2020)
  • Author(s): Miki Senda
  • Organizer: American Crystallographic Association (ACA) 2020
  • Int'l Joint Research
• [Presentation] 良質なタンパク質結晶と回折データを効率的に得るための戦略 (2020)
  • Author(s): 千田美紀
  • Organizer: 日本結晶学会令和2年度年会
• [Presentation] タンパク質結晶化の総合戦略 (2019)
  • Author(s): 千田美紀、千田俊哉
  • Organizer: 第19回蛋白質科学会年会
  • Invited
• [Presentation] Comprehensive strategy for efficient generation of well-diffracted crystals (2019)
  • Author(s): Miki Senda, Toshiya Senda
  • Organizer: ACA2019
  • Int'l Joint Research
• [Presentation] 良質なタンパク質結晶を得るための戦略 (2019)
  • Author(s): 千田美紀
  • Organizer: 平成30年度第2回構造生物学研究会
  • Invited
• [Presentation] Crystallization strategy when no crystals are obtained in the initial screening, (2018)
  • Author(s): Miki Senda, Toshiya Senda
  • Organizer: Structural Biology 2018
  • Int'l Joint Research
• [Presentation] 良質なタンパク質結晶と回折データを効率的に得るための戦略 (2018)
  • Author(s): 千田美紀、千田俊哉
  • Organizer: 結晶学会平成30年度年会
• [Presentation] Crystallization strategy when no well-diffracted crystals are obtained in the crystallization screening. (2018)
  • Author(s): Miki Senda, Toshiya Senda
  • Organizer: American Crystallographic Association (ACA) 2018
  • Int'l Joint Research
• [Remarks]
  • URL: https://www2.kek.jp/imss/sbrc/result/publication/