Structural analysis of transcription factor TFIIH subcomplex

• Project/Area Number: 22770110
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: Kagawa University (2013); University of Hyogo (2010-2012)
• Principal Investigator: KOMORI Hirofumi 香川大学, 教育学部, 准教授 (30382261)
• Project Period (FY): 2010-04-01 – 2014-03-31
• Project Status: Completed (Fiscal Year 2013)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2013: ¥650,000 (Direct Cost: ¥500,000、Indirect Cost: ¥150,000); Fiscal Year 2012: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2011: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000); Fiscal Year 2010: ¥1,170,000 (Direct Cost: ¥900,000、Indirect Cost: ¥270,000)
• Keywords: タンパク質 / Ｘ線結晶構造解析 / 結晶 / 転写因子 / タンパク質の精製 / タンパク質複合体 / X線結晶解析 / TFIIH / TFIIE

Research Abstract

The purpose of this study is to determine the three-dimensional structures of transcription factors by X-ray crystallographic analysis, in order to understand the molecular mechanism of the DNA transcriptional regulation with RNA polymerase II. Transcription factors function as a complex of various kinds of proteins. To prepare the sample suitable for crystallization, the purification of the significant protein complex involved in transcriptional regulation was performed by using a co-expression system of E. coli and insect cells.

Research Products

• [Journal Article] New insights into the catalytic active site structure of multicopper oxidase (2014)
  • Author(s): H. Komori, R. Sugiyama, K. Kataoka, K. Miyazaki, Y. Higuchi & T. Sakurai
  • Journal Title: Acta Cryst. D Volume: 70 Pages: 772-779
  • NAID: 120005451980
• [Journal Article] Inhibitory activity of Filipendula ulmaria constituents on recombinant human histidine decarboxylase (2013)
  • Author(s): Y. Nitta, H. Kikuzakic, T. Azuma, Y. Ye, M. Sakaue, Y. Higuchi, H. Komori, & H. Ueno
  • Journal Title: Food Chemistry Volume: 138 Pages: 1551-1556
• [Journal Article] Photosensitivity of the Ni-A state of [NiFe] hydrogenase from D. vulgaris Miyazaki F with visible light (2013)
  • Author(s): H. Osuka, Y. Shomura, H. Komori, N. Shibata, S. Nagao, Y. Higuchi, & S. Hirota
  • Journal Title: Biochem. Biophys. Res. Commun Volume: 430 Pages: 284-288
• [Journal Article] Cyrstal structure of the CueO mutants at Glu506, the key amino acid located in the proton transfer pathway for dioxygen reduction (2013)
  • Author(s): H. Komori, T. Kajikawa, K. Kataoka, Y. Higuchi & T. Sakurai
  • Journal Title: Biochem. Biophys. Res. Commun Volume: 438 Pages: 686-690
• [Journal Article] Formation of Oligomeric Cytochrome c during Folding by Intermolecular Hydrophobic Interaction between Nand C-Terminal α-Helices (2013)
  • Author(s): P. P. Parui, M. Deshpande, S. Nagao, H. Kamikubo, H. Komori, Y. Higuchi, M. Kataoka, & S. Hirota
  • Journal Title: Biochemistry Volume: 52 Pages: 8732-8744
• [Journal Article] Cyrstal structure of the CueO mutants at Glu506, the key amino acid located in the proton transfer pathway for dioxygen reduction (2013)
  • Author(s): H. Komori, T. Kajikawa, K. Kataoka, Y. Higuchi & T. Sakurai
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 438 Issue: 4 Pages: 686-690
  • DOI: 10.1016/j.bbrc.2013.07.121
  • Peer Reviewed
• [Journal Article] An O-Centered Structure of the Trinuclear Copper Center in the Cys500Ser/Glu506Gln Mutant of CueO and Structural Changes in Low to High X-Ray Dose Conditions (2012)
  • Author(s): H. Komori, R. Sugiyama, K. Kataoka, Y. Higuchi & T. Sakurai
  • Journal Title: Angew chem Volume: 51 Pages: 1861-1864
  • NAID: 120003959483
• [Journal Article] Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from B. subtilis (2012)
  • Author(s): Y. Shomura, E. Hinokuchi, H. Ikeda, A. Senoo, Y. Takahashi, J. Saito, H. Komori, N. Shibata, Y. Yonetani, & Y. Higuchi
  • Journal Title: Protein Sci Volume: 21 Pages: 707-716
• [Journal Article] Purification, crystallization and preliminary X-ray analysis of human histidine decarboxylase (2012)
  • Author(s): H. Komori, Y. Nitta, H. Ueno, & Y. Higuchi
  • Journal Title: Acta Cryst. F Volume: 68 Pages: 675-677
• [Journal Article] Structural study reveals Ser345 determines substrate specificity on human histidine (2012)
  • Author(s): H. Komori, Y. Nitta, H. Ueno, & Y. Higuchi
  • Journal Title: J. Biol. Chem Volume: 287 Pages: 29715-19183
• [Journal Article] Domain swapping of the heme and N-terminal α-helix in Hydrogenobacter thermophilus cytochrome c552 dimer (2012)
  • Author(s): Y. Hayashi, S. Nagao, H. Osuka, H. Komori, Y. Higuchi, & S. Hirota
  • Journal Title: Biochemistry Volume: 52 Pages: 8608-8616
• [Journal Article] An O-centered structure of the trinuclear copper center in the Cys500Ser/Glu506Gln mutant of CueO and structural changes in low to high X-ray dose conditions. (2012)
  • Author(s): Komori H, Sugiyama R, Kataoka K, Higuchi Y, Sakurai T.
  • Journal Title: Angew Chem Int Ed Engl. Volume: 51 Pages: 1861-1864
  • NAID: 120003959483
  • Peer Reviewed
• [Journal Article] Structural and enzymatic characterization of BacD, an L-amino acid dipeptide ligase from Bacillus subtilis. (2012)
  • Author(s): Shomura Y, Hinokuchi E, Ikeda H, Senoo A, Takahashi Y, Saito J, Komori H, Shibata N, Yonetani Y, Higuchi Y.
  • Journal Title: Protein Sci. Volume: 21 Pages: 707-716
  • Peer Reviewed
• [Journal Article] Purification, crystallization and preliminary X-ray analysis of human histidine decarboxylase (2012)
  • Author(s): Komori H, Nitta Y, Ueno H, Higuchi Y.
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun. Volume: 68 Pages: 675-677
  • Peer Reviewed
• [Journal Article] Structural study reveals that Ser-354 determines substrate specificity on human histidine decarboxylase. (2012)
  • Author(s): Komori H, Nitta Y, Ueno H, Higuchi Y.
  • Journal Title: J Biol Chem. Volume: 287 Pages: 29175-29183
  • Peer Reviewed
• [Journal Article] Domain swapping of the heme and N-terminal α-helix in Hydrogenobacter thermophilus cytochrome c(552) dimer. (2012)
  • Author(s): Hayashi Y, Nagao S, Osuka H, Komori H, Higuchi Y, Hirota S.
  • Journal Title: Biochemistry. Volume: 51 Pages: 8608-8616
  • Peer Reviewed
• [Journal Article] Photosensitivity of the Ni-A state of [NiFe] hydrogenase from Desulfovibrio vulgaris Miyazaki F with visible light. (2012)
  • Author(s): Osuka H, Shomura Y, Komori H, Shibata N, Nagao S, Higuchi Y, Hirota S.
  • Journal Title: Biochem Biophys Res Commun. Volume: 430 Pages: 284-288
  • NAID: 120005716864
  • Peer Reviewed
• [Journal Article] Inhibitory activity of Filipendula ulmaria constituents on recombinant human histidine decarboxylase. (2012)
  • Author(s): Nitta Y, Kikuzaki H, Azuma T, Ye Y, Sakaue M, Higuchi Y, Komori H, Ueno H.
  • Journal Title: Food Chem. Volume: 138 Pages: 1551-1556
  • Peer Reviewed
• [Journal Article] Positively charged residues located downstream of PIP-box, together with TD amino acids within PIP-box, are important for CRL4Cdt2-mediated proteolysis (2011)
  • Author(s): M. Michishita, A. Morimoto, T. Ishii, H. Komori, Y. Higuchi, Y. Shiomi & H. Nishitani
  • Journal Title: Genes Cells Volume: 16 Pages: 12-22
• [Journal Article] Crystallographic characterization of the DIX domain of the Wnt signalling positive regulator Ccd1 (2011)
  • Author(s): S. Terawaki, K. Yano, T. Katsutani, K. Shiomi, K. Keino-Masu, M. Masu, Y. Shomura, H. Komori, N. Shibata & Y. Higuchi
  • Journal Title: Acta Cryst. F Volume: 67 Pages: 758-761
• [Journal Article] Role of π-Electron Systems in Stabilization of the Oxidized Tetraheme Architecture in Cytochrome c3 and Structural Changes in Low to High X-Ray Dose Conditions (2011)
  • Author(s): Y. Takayama, M. Taketa-Sato, H. Komori, K. Morita, SJ. Kang, Y. Higuchi, & H. Akutsu
  • Journal Title: Bulletin of the Chemical Society of Japan Volume: 841 Pages: 1096-1101
• [Journal Article] Crystal structures of ethanolamine ammonia-lyase complexed with coenzyme B12 analogs and substrates (2010)
  • Author(s): N. Shibata, H. Tamagaki, S. Ohtsuki, N. Hieda, K. Akita, H. Komori, Y. Shomura, S. Terawaki, K. Mori, N. Yasuoka, Y. Higuchi & T. Toraya
  • Journal Title: J. Biol. Chem Volume: 285 Pages: 26484-26493
• [Journal Article] Cytochrome c polymerization by successive domain swapping at the C-terminal helix (2010)
  • Author(s): S. Hirota, Y. Hattori, S. Nagao, M. Taketa, H. Komori, H. Kamikubo, Z. Wang, I. Takahashi, S. Negi, Y. Sugiura, M. Kataoka & Y. Higuchi
  • Journal Title: Proc. Natl. Acad. Sci. USA Volume: 107 Pages: 12854-12859
  • NAID: 120005716875
• [Journal Article] Crystallization and preliminary X-ray analysis of dimeric and trimeric cytochromes c from horse heart (2010)
  • Author(s): M. Taketa, H. Komori, Y. Hattori, S. Nagao, S. Hirota, & Y. Higuchi
  • Journal Title: Acta Cryst. F Volume: 66 Pages: 1477-1479
• [Journal Article] Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3 (2010)
  • Author(s): R. Nishimasu, H. Komori, Y. Higuchi, H. Nishimasu & H. Hiroaki
  • Journal Title: Kobe J Med Sci Volume: 56
  • NAID: 110009824994
• [Journal Article] Crystal structure analysis of Bacillus subtilis ferredoxin-NADP+ oxidoreductase and the structural basis for its substrate selectivity (2010)
  • Author(s): H. Komori, D. Seo, T. Sakurai & Y. Higuchi
  • Journal Title: Protein Sci Volume: 19 Pages: 2279-2290
• [Presentation] 構造解析に向けた鉄調節性転写因子の精製 (2013)
  • Author(s): 小森 博文
  • Organizer: 日本生物高分子学会2013年度大会
  • Place of Presentation: 大阪
• [Presentation] ヒト由来ヒスチジン脱炭酸酵素の構造解析 (2012)
  • Author(s): 小森博文
  • Organizer: 日本生化学会
  • Place of Presentation: 福岡国際会議場・マリンメッセ福岡（福岡県）
• [Presentation] Ｘ線照射によるマルチ銅活性中心の構造変化 (2012)
  • Author(s): 小森博文
  • Organizer: 日本結晶学会
  • Place of Presentation: 東北大学(宮城県）
• [Presentation] Structural basis for the histamine synthesis by human histidine decarboxylase (2012)
  • Author(s): Hirofumi Komori
  • Organizer: Asian Crystallographic Association
  • Place of Presentation: Adelaide (Australia)
• [Presentation] マルチ銅酸化酵素の構造解析 (2011)
  • Author(s): 小森博文
  • Organizer: 生化学会
  • Place of Presentation: 国立京都国際会館(京都府)
  • Year and Date: 2011-09-22
• [Presentation] Reconstitution of the subcomplex of yeast TFIIH (2010)
  • Author(s): 小森博文
  • Organizer: 1st HFSP Alumni Meeting Japan
  • Place of Presentation: 東京大学(東京都)
  • Year and Date: 2010-10-09
• [Presentation] 構造解析に向けた鉄調節性転写因子の精製
  • Author(s): 小森 博文
  • Organizer: 日本生物高分子学会2013年度大会
• [Remarks]
  • URL: http://www.ed.kagawa-u.ac.jp/~komori/
• [Remarks] 研究内容 - 小森研究室
  • URL: http://www.ed.kagawa-u.ac.jp/~komori/research.html