Structural biology of polyubuiquitin chain recognition

• Project/Area Number: 21687009
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: FUKAI Shuya 東京大学, 放射光連携研究機構, 准教授 (10361792)
• Project Period (FY): 2009 – 2011
• Project Status: Completed (Fiscal Year 2011)
• Budget Amount: ¥27,300,000 (Direct Cost: ¥21,000,000、Indirect Cost: ¥6,300,000); Fiscal Year 2011: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2010: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2009: ¥17,680,000 (Direct Cost: ¥13,600,000、Indirect Cost: ¥4,080,000)
• Keywords: X線結晶構造解析 / ユビキチン / 分子間相互作用 / 炎症シグナル / DNA損傷応答 / シグナル伝達 / 生体分子 / 蛋白質 / 分子認識

Research Abstract

Ubiquitin is well-known as a label for protein degradation. Recent studies have showed that ubiquitin functions as labels for various cellular processes besides the protein degradation. In this research, we determined three-dimensional structures of complexes comprising ubiquitin and its binding proteins and showed how ubiquitin is recognized during responses towards DNA damage and inflammation.

Research Products

• [Journal Article] Specific recognition of linear ubiquitin chains by the Npl4 zinc finger(NZF) domain of the HOIL-1L subunit of the linear ubiquitin chain assembly complex (2011)
  • Author(s): Sato, Y., Fujita, H., Yoshikawa, A., Yamashita, M., Yamagata, A., Kaiser, S. E., Iwai, K., Fukai, S
  • Journal Title: Proceedings of National Academy of Science United States of America Volume: 108巻 Issue: 51 Pages: 20520-20525
  • DOI: 10.1073/pnas.1109088108
  • Peer Reviewed
• [Journal Article] tructure and function of SecDF, a protein export-enhancing membrane component (2011)
  • Author(s): Tsukazaki, T., et al
  • Journal Title: Nature Volume: 475 Issue: 7350 Pages: 235-238
  • DOI: 10.1038/nature09980
  • Peer Reviewed
• [Journal Article] Structural insight into the membrane insertion of tail-anchored proteins by Get3 (2010)
  • Author(s): Yamagata, A., Mimura, H., Sato, Y., Yamashita, M., Yoshikawa, A., Fukai, S.
  • Journal Title: Genes to Cells 15 Pages: 29-41
  • Peer Reviewed
• [Journal Article] Structural basis for the Rho-and phosphoinositide-dependent localization of the exocyst subunit Sec3 (2010)
  • Author(s): Yamashita, M., Kurokawa, K., Sato, Y., Yamagata, A., Mimura, H., Yoshikawa, A., Sato, K., Nakano. A.. Fukai. S.
  • Journal Title: Nature Structural & Molecular Biology 17 Pages: 180-186
  • Peer Reviewed
• [Journal Article] Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3 (2009)
  • Author(s): Sato, Y., Yoshikawa, A., Yamashita, M., Yamagata, A., Fukai, S.
  • Journal Title: The EMBO Journal Volume: 28巻 Issue: 24 Pages: 3903-3909
  • DOI: 10.1038/emboj.2009.345
  • Peer Reviewed
• [Journal Article] Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin (2009)
  • Author(s): Yoshikawa, A., Sato, Y., Yamashita, M., Mimura, H., Yamagata, A., Fukai, S.
  • Journal Title: FEBS Letters. Volume: 583巻 Issue: 20 Pages: 3317-3322
  • DOI: 10.1016/j.febslet.2009.09.028
  • Peer Reviewed
• [Journal Article] Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80 (2009)
  • Author(s): Sato, Y., Yoshikawa, A., Mimura, H., Yamashita, M., Yamagata, A., Fukai, S.
  • Journal Title: The EMBO Journal Volume: 28巻 Issue: 16 Pages: 2461-2468
  • DOI: 10.1038/emboj.2009.160
  • Peer Reviewed
• [Journal Article] Tuberous sclerosis tumor suppressor complex-like complexes act as GTPase-activating proteins for Ral GTPases (2009)
  • Author(s): Shirakawa, R., Fukai, S., Kawato, M., Higashi, T., Kondo, H., Ikeda, T., Nakayama, E., Okawa, K., Nureki, O., Kimura, T., Kita, T., Horiuchi. H.
  • Journal Title: The Journal of Biological Chemistry 284 Pages: 21580-21588
  • Peer Reviewed
• [Journal Article] Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by tandem UIMs of RAP80 (2009)
  • Author(s): Sato, Y., Yoshikawa, A., Mimura, H., Yamashita, M., Yamagata, A., Fukai, S.
  • Journal Title: The EMBO Journal 28 Pages: 2461-2468
  • Peer Reviewed
• [Journal Article] Mechanism for the definition of elongation and termination by the class 11 CCA-adding enzyme (2009)
  • Author(s): Toh, Y., Takeshita, D., Numata, T., Fukai, S., Nureki, O., Tomita, K.
  • Journal Title: The EMBO Journal 28 Pages: 3353-3365
  • Peer Reviewed
• [Journal Article] Crystal structure of the NEMO ubiquitin-binding domain in complex with Lys 63-linked di-ubiquitin (2009)
  • Author(s): Yoshikawa, A., Sato, Y., Yamashita, M., Mimura, H., Yamagata, A., Fukai, S.
  • Journal Title: FEBS Letters 583 Pages: 3317-3322
  • Peer Reviewed
• [Journal Article] Structural basis for specific recognition of Lys 63-linked polyubiquitin chains by NZF domains of TAB2 and TAB3 (2009)
  • Author(s): Sato, Y., Yoshikawa, A., Yamashita, M., Yamagata, A., Fukai, S.
  • Journal Title: The EMBO Journal 28 Pages: 3903-3909
  • Peer Reviewed
• [Presentation] 構造解析のためのユビキチン鎖の大量合成 (2011)
  • Author(s): 深井周也
  • Organizer: 第11回日本蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポパーク
  • Year and Date: 2011-06-09
• [Presentation] 構造解析のためのユビキチン鎖の大量合成 (2011)
  • Author(s): 深井周也
  • Organizer: 第11回日本蛋白質科学会年会
  • Place of Presentation: ホテル阪急エキスポパーク(大阪府吹田市)(招待講演)
  • Year and Date: 2011-06-09
• [Presentation] Structural basis of ubiquitinchain recognition by NZF domains for NF-κB activation (2011)
  • Author(s): 深井周也
  • Organizer: TNF2011
  • Place of Presentation: 淡路夢舞台国際会議場
  • Year and Date: 2011-05-18
• [Presentation] Structural basis of ubiquitin chain recognition by NZF domains for NF-κB activation (2011)
  • Author(s): 深井周也
  • Organizer: TNF2011(第13回国際TNF会議)
  • Place of Presentation: 淡路夢舞台国際会議場(兵庫県淡路市)(招待講演)
  • Year and Date: 2011-05-18
• [Presentation] Mechanisms for recognitionof K63-linked polyubiquitin chains (2010)
  • Author(s): 深井周也
  • Organizer: Pacifichem2010
  • Place of Presentation: ハワイコンベンションセンター
  • Year and Date: 2010-12-19
• [Presentation] Mechanisms for recognition of K63-linked polyubiquitin chains (2010)
  • Author(s): 深井周也
  • Organizer: Pacifichem2010
  • Place of Presentation: 大阪大学コンベンションセンター(吹田キャンパス)
  • Year and Date: 2010-12-19
• [Presentation] 繋留複合体による膜融合制御の構造基盤 (2010)
  • Author(s): 深井周也
  • Organizer: BMB2010
  • Place of Presentation: 神戸ポートピアランド
  • Year and Date: 2010-12-10
• [Presentation] Znフィンガーによるユビキチン鎖識別のメカニズム (2010)
  • Author(s): 深井周也
  • Organizer: 平成22年度日本結晶学会年会
  • Place of Presentation: 大阪大学
  • Year and Date: 2010-12-05
• [Presentation] Znフィンガーによるユビキチン鎖識別のメカニズム (2010)
  • Author(s): 深井周也
  • Organizer: 平成22年度日本結晶学会年会
  • Place of Presentation: 大阪大学コンベンションセンター(吹田キャンパス)
  • Year and Date: 2010-12-05
• [Presentation] ユビキチン化シグナルを読み解くユビキチン受容体の構造生物学 (2010)
  • Author(s): 深井周也
  • Organizer: 文部科学省科研費特定領域研究「タンパク質分解」公開シンポジウム
  • Place of Presentation: 東京ガーデンパレス
  • Year and Date: 2010-08-21
• [Presentation] Lys63結合型ポリユビキチン鎖認識のメカニズム (2009)
  • Author(s): 深井周也
  • Organizer: 第32回日本分子生物学会年会
  • Place of Presentation: パシフィコ横浜
  • Year and Date: 2009-12-10
• [Presentation] 低分子量GTPaseによる開口放出制御の構造基盤 (2009)
  • Author(s): 深井周也
  • Organizer: 第9回日本蛋白質科学会年会
  • Place of Presentation: 熊本全日空ホテルニュースカイ
  • Year and Date: 2009-05-22
• [Book] 細胞工学29巻[特集]ユビキチン修飾系の多彩な機能 (2010)
  • Author(s): 深井周也
  • Publisher: 秀潤社
• [Book] 日本結晶学会誌52巻特集構造生物学研究の新展開 (2010)
  • Author(s): 佐藤裕介,深井周也
  • Publisher: 日本結晶学会
• [Book] 細胞工学 29巻[特集]ユビキチン修飾系の多彩な機能 (2010)
  • Author(s): 深井周也
  • Publisher: 秀潤社
• [Book] 日本結晶学会誌52巻特集構造生物学研究の新展開 (2010)
  • Author(s): 佐藤裕介, 深井周也
  • Publisher: 日本結晶学会
• [Book] 生体の科学60巻[特集]ユビキチン化による生体機能の調節 (2009)
  • Author(s): 佐藤裕介,深井周也
  • Publisher: 金原一郎記念医学医療振興財団/医学書院
• [Book] 生化学 (2009)
  • Author(s): 深井周也
  • Publisher: 日本生化学会
• [Book] 生化学81巻みにれびゅう (2009)
  • Author(s): 深井周也
  • Publisher: 日本生化学会
• [Book] 生体の科学60巻[特集]ユビキチン化による生体機能の調節 (2009)
  • Author(s): 佐藤裕介, 深井周也
  • Publisher: 金原一郎記念医学医療振興財団/医学書院
• [Remarks]
  • URL: http://www.iam.u-tokyo.ac.jp/srro/