Molecular basis of the adaptor domains from AAA-ATPases for locating organelles.

• Project/Area Number: 16570136
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Biophysics
• Research Institution: Yokohama City University
• Principal Investigator: HIROAKI Hidekazu Yokohama City University, International Graduate School of Arts and Sciences, Ph.D., Associated Professor, 大学院・国際総合科学研究科, 準教授 (10336589)
• Project Period (FY): 2004 – 2005
• Project Status: Completed (Fiscal Year 2005)
• Budget Amount: ¥3,600,000 (Direct Cost: ¥3,600,000); Fiscal Year 2005: ¥1,500,000 (Direct Cost: ¥1,500,000); Fiscal Year 2004: ¥2,100,000 (Direct Cost: ¥2,100,000)
• Keywords: functional protein domains / Nuclear magnetic resonance (NMR) / protein domain anatomy / late endosome / tubulin / cell skeleton / MIT domain / sequence identity / プロテアソーム / ポリユビキチン / ペルオキシソーム / X線結晶構造解析

Research Abstract

AAA-ATPases are well conserved molecular machines from bacteria to human, which alters the conformations and/or multimerization states of substrate proteins with an ATP-depending manner. AAA-ATPases are characterized as harboring one or several "AAA" domains at their central region of the molecules, whereas various N-terminus domains may be responsible for differentiating their specific functions. I have hypothesized that some of them can be responsible not only for their substrate specificity, but also for their subcellular location. In order to solve this problem, so-called "protein domain anatomy" approach was taken.
As a result, first we have identified a novel domain from the PEX1 N-terminal region. Surprisingly, although below 15% of sequence identity found to VCP and NSF, the structure of PEX1NTD is very similar to those corresponding domains. Second, we have identified the solution structures from N-terminal MIT domain of Vps4 type I AAA-ATPase and its distant homolog katanin p60. These domains adopted into an up-and-down three helix bundle fold with a characteristic cleft on the molecular surface, which may act as a ligand binding site, katanin p60 N-terminal domain was associated with a coiled-coil region, which should be designed prior to structural analysis. Some other AAA-ATPases require a shuttle factor molecule instead of its own adaptor domain. From one of them, we determined the solution structure of UBA domain from Dsk2 protein, an adaptor of 19S proteosome, in complex with ubiquitin. In addition, molecular rigidity and flexibility of K48- and K63-linked tetra ubiquitin chain were compared by using solution NMR.
Finally, two domains of the five examined systems were found to have affinities to phosphoinositides. This suggested the domains share a function for associating organellar membranes.

Research Products

• [Journal Article] ペルオキシソーム因子PEX1 ATPaseのN末端ドメインの立体構造が示したAAA ATPase間の進化的類縁関係 (2006)
  • Author(s): 廣明 秀一, 塩澤久美子, 富井健太郎
  • Journal Title: 生物物理 46(3) Pages: 159-163
  • NAID: 110004750171
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] The Structure of N-terminal Domain from PEX1 Reveals Its Evolutionary Relationship to Type II AAA-ATPases (2006)
  • Author(s): Shiozawa, K., Tomii, K., Hiroaki, H^*
  • Journal Title: SEIBUTSUBUTSURI (Biophysics, Jpn.Ed.) 46 Pages: 159-163
  • NAID: 110004750171
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] ペルオキシソーム因子PEX1 ATPaseのN末端ドメインの立体構造が示したAAA ATPase間の進化的類縁関係 (2006)
  • Author(s): 廣明 秀一, 塩澤久美子, 富井健太郎
  • Journal Title: 生物物理 46(3)(印刷中)
  • NAID: 110004750171
• [Journal Article] Continuous Designed Cation-pi Interactions Increase the Thermal Stability of an α-Helical Coiled-coil. (2005)
  • Author(s): Sakurai, Y., Mizuno, T., Hiroaki, H., Gohda, K., Oku, J.I., Tanaka, T^*.
  • Journal Title: Angewandte Chemie International Edition 44 Pages: 6180-6183
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structural characterization of the MIT domain from human Vps4b. (2005)
  • Author(s): Takasu, H., Jee, J.G., Ohno, A., Goda, N., Fujiwara, K., Tochio, H., Shirakawa, M., Hiroaki, H^*
  • Journal Title: Biochemistry Biophysics Research Communnication 334 Pages: 460-465
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structure of the UBA domain of Dsk2p in complex with Ubiquitin : Molecular Determinants for Ubiquitin Recognition. (2005)
  • Author(s): Ohno, A., Jee, J., Fujiwara, K., Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H., Shirakawa, M^*
  • Journal Title: Structure 13 Pages: 1-12
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Continuous Designed Cation-pi Interactions Increase the Thermal Stability of an α-Helical Coiled-coil. (2005)
  • Author(s): Sakurai, Y., Mizuno, T., Hiroaki, H., Gohda, K., Oku, J.I., Tanaka, T^*.
  • Journal Title: Angewandte Chem Int Ed. 44 Pages: 6180-6183
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural characterization of the MIT domain from human Vps4b. (2005)
  • Author(s): Takasu, H., Jee, J.G., Ohno, A., Goda, N., Fujiwara, K., Tochio, H., Shirakawa, M., Hiroaki H^*.
  • Journal Title: Biochem Biophys Res Commun. 334 Pages: 460-465
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the UBA domain of Dsk2p in complex with Ubiquitin : Molecular Determinants for Ubiquitin Recognition. (2005)
  • Author(s): Ohno, A., Jee, J., Fujiwara, K., Tenno, T., Goda, N., Tochio, H., Kobayashi, H., Hiroaki, H..Shirakawa, M^*.
  • Journal Title: Structure 13 Pages: 1-12
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Optimization of size complementary of the aromatic side chain in the hydrophobic core of the designed coiled-coil. (2005)
  • Author(s): Sakurai, Y., Mizuno, T., Hiroaki H., Oku, J.I., Tanaka, T^*
  • Journal Title: J Pept Res 66 Pages: 387-394
• [Journal Article] Continuous Designed Cation-pi Interactions Increase the Thermal Stability of an α-Helical Coiled-coil. (2005)
  • Author(s): Sakurai, Y., Mizuno, T., Hiroaki, H., Gohda, K., Oku, J.I., Tanaka, T^*.
  • Journal Title: Angewandte Chem Int Ed 44 Pages: 6180-6183
• [Journal Article] Structural characterization of the MIT domain from human Vps4b. (2005)
  • Author(s): Takasu, H., Jee, J.G., Ohno, A., Goda, N., Fujiwara, K., Tochio, H., Shirakawa, M., Hiroaki, H^*
  • Journal Title: Biochem Biophys Res Commun 334 Pages: 460-465
• [Journal Article] Crystallographic characterization of the N-terminal domain of PEX1. (2004)
  • Author(s): Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H.
  • Journal Title: Acta Crystallography D, Biological Crystallography. 60(11) Pages: 2098-2099
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains. (2004)
  • Author(s): Tenno T, Fujiwara K, Tochio H, Iwai K, Morita EH, Hayashi H, Murata S, Hiroaki H, Sato M, Tanaka K, Shirakawa M.
  • Journal Title: Genes to Cells. 9(10) Pages: 865-875
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. (2004)
  • Author(s): Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H.
  • Journal Title: Journal of Biological Chemistry. 279(48) Pages: 50060-50068
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] High-throughput construction method for expression vector of peptides for NMR study suited for isotopic labeling. (2004)
  • Author(s): Tenno T, Goda N, Tateishi Y, Tochio H, Mishima M, Hayashi H, Shirakawa M, Hiroaki H.
  • Journal Title: Protein Engineering Design and Selection. 17(4) Pages: 305-314
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Crystallographic characterization of the N-terminal domain of PEX1. (2004)
  • Author(s): Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Tochio, H., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H^*.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. 60 Pages: 2098-2099
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains. (2004)
  • Author(s): Tenno, T., Fujiwara, K., Tochio, H., Iwai, K., Morita, E.H., Hayashi, H., Murata, S., Hiroaki, H., Sato, M., Tanaka, K., Shirakawa, M^*.
  • Journal Title: Genes to Cells 9 Pages: 865-875
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Structure of the N-terminal domain of PEX1 AAA-ATPase : characterization of a putative adaptor-binding domain. (2004)
  • Author(s): Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Tochio, H., Akiyama, Y., Shimizu, T., Shirakawa, M., Hiroaki, H^*.
  • Journal Title: J Biol Chem. 279 Pages: 50060-50068
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A vector suited to high-throughput expression of isotopically-labeled peptides. (2004)
  • Author(s): Tenno, T., Goda, N., Tateishi, Y., Tochio, H., Mishima, M., Hayashi, H., Shirakawa, M., Hiroaki, H^*.
  • Journal Title: Protein Eng Design Sel. 17 Pages: 305-304
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Crystallographic characterization of the N-terminal domain of PEX1. (2004)
  • Author(s): Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H.
  • Journal Title: Acta Crystallogr D Biol Crystallogr. 60(11) Pages: 2098-2099
• [Journal Article] Structural basis for distinct roles of Lys63- and Lys48-linked polyubiquitin chains. (2004)
  • Author(s): Tenno T, Fujiwara K, Tochio H, Iwai K, Morita EH, Hayashi H, Murata S, Hiroaki H, Sato M, Tanaka K, Shirakawa M.
  • Journal Title: Genes Cells. 9(10) Pages: 865-875
• [Journal Article] Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. (2004)
  • Author(s): Shiozawa K, Maita N, Tomii K, Seto A, Goda N, Akiyama Y, Shimizu T, Shirakawa M, Hiroaki H.
  • Journal Title: J Biol Chem. 279(48) Pages: 50060-50068
• [Journal Article] High-throughput construction method for expression vector of peptides for NMR study suited for isotopic labeling. (2004)
  • Author(s): Tenno T, Goda N, Tateishi Y, Tochio H, Mishima M, Hayashi H, Shirakawa M, Hiroaki H.
  • Journal Title: Protein Eng Des Sel. 17(4) Pages: 305-314
• [Patent(Industrial Property Rights)] ヒトVps4bのMITドメインと二価または三価の金属イオン複合体の構造的特徴およびヒトVps4bのMITドメインによるホスファチジルイノシトールリン酸認識機構 (2004)
  • Inventor(s): 白川昌宏, 廣明秀一, 高須博敏
  • Industrial Property Rights Holder: 横浜市立大学
  • Industrial Property Number: 2004-350635
  • Filing Date: 2004-12-03
  • Description: 「研究成果報告書概要(和文)」より