Structural analysis of the intracellular proteolytic system

2010 Fiscal Year Final Research Report

• Project Area: Proteolysis in the Regulation of Biological Processes
• Project/Area Number: 18076003
• Research Category: Grant-in-Aid for Scientific Research on Priority Areas
• Allocation Type: Single-year Grants
• Review Section: Biological Sciences
• Research Institution: Kyoto University
• Principal Investigator: TOCHIO Hidehito Kyoto University, 大学院・工学研究科, 准教授 (70336593)
• Co-Investigator(Kenkyū-buntansha): KURIMOTO Eiji 名古屋市立大学, 大学院・薬学研究科, 研究員 (90234575) ; NODA Nobuo 北海道大学, 大学院・薬学研究科, 助教 (40396297) ; YAMAGUCHI Yoshiki 理化学研究所, チームリーダー (90323451)
• Project Period (FY): 2006 – 2010
• Keywords: X線結晶構造解析 / オートファジー / ユビキチン / NMR / 中性子小角散乱

Research Abstract

Structural studies of proteins and protein complexes related to the ubiquitin-proteasome system and autophagy were conducted using X-ray crystallography, NMR and small-angle neutron scattering techniques. The details of the ubiquitin interaction mode of ubiquitin receptors,the working mechanism of E2 (UbcH5b) and the activation mechanism of SCF E3 by NEDD8 were revealed. We also determined the structures of deconjugating enzyme Atg4B bound to LC3, E1-like enzyme Atg7, Atg12-Atg5 conjugate, and Atg8-Atg19 and LC3-p62 complexes, clarifying the molecular mechanisms of reversible Atg8 lipidation and autophagic receptor recognition byAtg8/LC3.

Research Products

• [Journal Article] Structural basis for regulation of poly-SUMO chain by a SUMO-like domain of Nip45 (2010)
  • Author(s): Sekiyama N, Arita K, Ikeda Y, Hashiguchi K, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M.
  • Journal Title: Proteins 78 Pages: 1491-1502
  • Peer Reviewed
• [Journal Article] Purification, crystallization and preliminary crystallographic studies of Lys48-linked polyubiquitin chains. (2010)
  • Author(s): Morimoto D, Isogai S, Tenno T, Tochio H, Shirakawa M, Ariyoshi M.
  • Journal Title: Acta Crystallograph Sect F Struct Biol Cryst Commun 66 Pages: 834-837
  • Peer Reviewed
• [Journal Article] Solution structure of a zinc-finger domain that binds to poly-ADP-ribose. (2010)
  • Author(s): Isogai S, Kanno S.I., Ariyoshi M, Tochio H, Ito Y, Yasui A, Shirakawa M.
  • Journal Title: Genes Cells 15 Pages: 101-110
  • Peer Reviewed
• [Journal Article] Distance Determination in Proteins inside Xenopus laevis Oocytes by Double Electron-Electron Resonance Experiments. (2010)
  • Author(s): Igarashi R, Sakai T, Hara H, Tenno T, Tanaka T, Tochio H, Shirakawa M.
  • Journal Title: J Am Chem Soc 132 Pages: 8228-8229
  • Peer Reviewed
• [Journal Article] SANS investigation of assembly state of proteasome activator 28and the 20S proteasome. (2010)
  • Author(s): Sugiyama M, Kurimoto E, Sahashi H, Sakata E, Morimoto Y, Itoh K, Mori K, Fukunaga T, Minami Y, Kato K.
  • Journal Title: J Phys Conf Ser 247 Pages: 012020
  • Peer Reviewed
• [Journal Article] Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates (2010)
  • Author(s): Sakata E, Satoh T, Yamamoto S, Yamaguchi Y, Yagi-Utsumi M, Kurimoto E, Tanaka K, Wakatsuki S, Kato K.
  • Journal Title: Structure 18 Pages: 138-147
  • Peer Reviewed
• [Journal Article] The dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy. (2010)
  • Author(s): Fujioka Y, Noda NN, Nakatogawa H, Ohsumi Y, Inagaki F.
  • Journal Title: J Biol Chem 285 Pages: 1508-15
  • Peer Reviewed
• [Journal Article] The NMR structure of the autophagy-related protein Atg8. (2010)
  • Author(s): Kumeta K, Watanabe M, Nakatogawa H, Yamaguchi M, Ogura K, Adachi W, Fujioka Y, Noda NN, Ohsumi Y, Inagaki F.
  • Journal Title: J Biomol NMR 47 Pages: 237-241
  • Peer Reviewed
• [Journal Article] Atg8-family interacting motif crucial for selective autophagy. (2010)
  • Author(s): Noda NN, Ohsumi Y, Inagaki F.
  • Journal Title: FEBS Lett 584 Pages: 1379-1385
  • Peer Reviewed
• [Journal Article] Autophagy-related protein 8 (Atg8) family interacting motif in Atg3 mediates the Atg3-Atg8 interaction and is crucial for the cytoplasm-to-vacuole targeting pathway. (2010)
  • Author(s): Yamaguchi M, Noda NN, Nakatogawa H, Kumeta H, Ohsumi Y, Inagaki F.
  • Journal Title: J Biol Chem 285 Pages: 29599-29607
  • Peer Reviewed
• [Journal Article] Selective transport of alpha-mannosidase by autophagic pathways: structural basis for cargo recognition by Atg19 and Atg34. (2010)
  • Author(s): Watanabe Y, Noda NN, Kumeta H, Suzuki K, Ohsumi Y, Inagaki F.
  • Journal Title: J Biol Chem 285 Pages: 30026-30033
  • Peer Reviewed
• [Journal Article] Molecular Basis for SUMOylation-dependent Regulation of DNA Binding Activity of Heat Shock Factor 2. (2009)
  • Author(s): Tateishi Y, Ariyoshi M, Igarashi R, Hara H, Mizuguchi K, Seto A, Nakai A, Kokubo T, Tochio H, Shirakawa M.
  • Journal Title: J Biol Chem 284 Pages: 2435-2447
  • Peer Reviewed
• [Journal Article] Structural basis for the multiple interactions of the MyD88 TIR domain in TLR4 signaling. (2009)
  • Author(s): Ohnishi H, Tochio H, Kato Z, Orii K.E., Li A.L., Kimura T, Hiroaki H, Kondo N, Shirakawa M.
  • Journal Title: Proc Natl Acad Sci 106 Pages: 10260-10265
  • Peer Reviewed
• [Journal Article] High-resolution multi-dimensional NMR spectroscopy of proteins in human cells. (2009)
  • Author(s): Inomata K, Ohno A, Tochio H, Isogai S, Tenno T, Nakase I, Takeuchi T, Futaki S, Ito Y, Hiroaki H., Shirakawa M.
  • Journal Title: Nature 458 Pages: 106-109
  • Peer Reviewed
• [Journal Article] Assembly State of Proteasome Activator 28in an Aqueous Solution as Studied by Small-Angle Neutron Scattering (2009)
  • Author(s): Sugiyama M, Kurimoto E, Morimoto Y, Sahashi H, Sakata E, Hamada K, Itoh K, Mori K, Fukunaga T, Minami Y, Kato K.
  • Journal Title: J Phys Soc Jpn 78 Pages: (124802)1-(124802)6
  • Peer Reviewed
• [Journal Article] The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. (2009)
  • Author(s): Satoo K, Noda NN(Co-first), Kumeta H, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F.
  • Journal Title: EMBO J 28 Pages: 1341-1350
  • Peer Reviewed
• [Journal Article] Crystallization of Saccharomyces cerevisiae alpha-mannosidase, a cargo protein of the Cvt pathway. (2009)
  • Author(s): Watanabe Y, Noda NN, Honbou K, Suzuki K, Sakai Y, Ohsumi Y, Inagaki F.
  • Journal Title: Acta Crystallograph Sect F Struct Biol Cryst Commun 65 Pages: 571-573
  • Peer Reviewed
• [Journal Article] ATG Systems from the Protein Structural Point of View. (2009)
  • Author(s): Noda NN, Ohsumi Y, Inagaki F.
  • Journal Title: Chem Rev 109 Pages: 1587-1598
  • Peer Reviewed
• [Journal Article] Structure of the Small Ubiquitin-like Modifier (SUMO)-interacting Motif of MBD1-containing Chromatin-associated Factor 1 Bound to SUMO-3. (2008)
  • Author(s): Sekiyama N, Ikegami T, Yamane T, Ikeguchi M, Uchimura Y, Baba D, Ariyoshi M, Tochio H, Saitoh H, Shirakawa M.
  • Journal Title: J Biol Chem 283 Pages: 35966-35975
  • Peer Reviewed
• [Journal Article] Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism. (2008)
  • Author(s): Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M.
  • Journal Title: Nature 455 Pages: 818-821
  • Peer Reviewed
• [Journal Article] Crystal structure of a chaperone complex that contributes to the assembly of yeast 20S proteasomes. (2008)
  • Author(s): Yashiroda H, Mizushima T, Okamoto K, Kameyama T, Hayashi H, Kishimoto T, Niwa S, Kasahara M, Kurimoto E, Sakata E, Takagi K, Suzuki A, Hirano Y, Murata S, Kato K, Yamane T, Tanaka K.
  • Journal Title: Nature Struct Mol Biol 15 Pages: 228-236
  • Peer Reviewed
• [Journal Article] In vitro reconstitution of plant ATG8 and ATG12 conjugation systems essential for autophagy. (2008)
  • Author(s): Fujioka Y, Noda NN, Fujii K, Yoshimoto K, Ohsumi Y, Inagaki F.
  • Journal Title: J Biol Chem 283 Pages: 1921-1928
  • Peer Reviewed
• [Journal Article] Crystallization of the Atg12-Atg5 conjugate bound to Atg16 by the free interface diffusion method. (2008)
  • Author(s): Noda NN, Fujioka Y, Ohsumi Y, Inagaki F.
  • Journal Title: J Synchrotron Radiat 15 Pages: 266-268
  • Peer Reviewed
• [Journal Article] Structural basis of target recognition by Atg8/LC3 during selective autophagy. (2008)
  • Author(s): Noda NN, Kumeta H, Nakatogawa H, Satoo K, Adachi W, Ishii J, Fujioka Y, Ohsumi Y, Inagaki F.
  • Journal Title: Genes Cells 13 Pages: 1211-1218
  • Peer Reviewed
• [Journal Article] Crystallization of the coiled-coil domain of Atg16 essential for autophagy. (2008)
  • Author(s): Fujioka Y, Noda NN, Matsushita M, Ohsumi Y, Inagaki F.
  • Journal Title: Acta Crystallograph Sect F Struct Biol Cryst Commun 64 Pages: 1046-1048
  • Peer Reviewed
• [Journal Article] Fbsl protects the malfolded glycoproteins from the attack of peptide:N-glycanase (2007)
  • Author(s): Yamaguchi Y, Hirao T, Sakata E, Kamiya Y, Kurimoto E, Yoshida Y, Suzuki T, Tanaka K, Kato K.
  • Journal Title: Biochem Biophys Res Commun 362 Pages: 712-716
  • Peer Reviewed
• [Journal Article] Direct interactions between NEDD8and ubiquitin E2 conjugating enzymes upregulate cullin-based E3 ligase activity (2007)
  • Author(s): Sakata E, Yamaguchi Y, Miyauchi Y, Iwai K, Chiba T, Saeki Y, Matsuda N, Tanaka K, Kato K
  • Journal Title: Nature Struct Mol Biol 14 Pages: 167-168
  • Peer Reviewed
• [Journal Article] The Atg12-Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. (2007)
  • Author(s): Hanada T, Noda NN, Satomi Y, Ichimura Y, Fujioka Y, Takao T, Inagaki F, Ohsumi Y.
  • Journal Title: J Biol Chem 282 Pages: 37298-37302
  • Peer Reviewed
• [Presentation] Structural basis of Atg8 activation and transfer to Atg3 by Atg7 (2011)
  • Author(s): Noda NN, Satoo K, Fujioka Y, Kumeta K, Ohsumi Y, Inagaki F.
  • Organizer: Cold Spring Harbor Laboratory Meeting, The Ubiquitin Family
  • Place of Presentation: Cold Spring Harbor, NY, USA.
  • Year and Date: 20110500
• [Presentation] 中性子散乱によるPA28複合体およびα7ホモリングの動的高次構造解析 (2011)
  • Author(s): 栗本英治
  • Organizer: 日本薬学会第131年会
  • Place of Presentation: 静岡
  • Year and Date: 2011-03-29
• [Presentation] Structural basis of selective autophagy. (2010)
  • Author(s): Noda NN
  • Organizer: 1^st Sino-Japan Symposium on Autophagy
  • Place of Presentation: Xi'an, China.
  • Year and Date: 20101000
• [Presentation] Structural analysis of the UBA domain of p62 and its interaction with ubiquitin. (2010)
  • Author(s): Tochio H
  • Organizer: Pacifichem 2010
  • Place of Presentation: Hawaii Convention Center, Honolulu, USA.
  • Year and Date: 2010-12-18
• [Presentation] p62UBAドメインの結晶構造とユビキチンとの相互作用 (2010)
  • Author(s): 杤尾豪人
  • Organizer: 第10回日本蛋白質科学会年会
  • Place of Presentation: 札幌
  • Year and Date: 2010-06-17
• [Presentation] Structural basis of target recognition during selective autophagy (2009)
  • Author(s): Noda NN, Ohsumi Y, Inagaki F.
  • Organizer: 5^th International Symposium on Autophagy
  • Place of Presentation: Otsu, Japan.
  • Year and Date: 20090900
• [Presentation] 重水素標識を利用した中性子小角散乱法によるプロテアソーム構成タンパク質PA28およびα7サブユニットの溶液構造解析 (2009)
  • Author(s): 栗本英治
  • Organizer: 第47回日本生物物理学会年会
  • Place of Presentation: 徳島
  • Year and Date: 2009-11-01
• [Presentation] Crystal Structure and Biochemical Characterization of the UBA Domain of p62 (Sequestosome 1) (2008)
  • Author(s): Tochio H
  • Organizer: ZOMES V:The Fifth International Symposium on the COP9 signalosome, Proteasome and eIF3: At the interface between signaling &proteolysis
  • Place of Presentation: RIKEN Yokohama Institute,Yokohama, Japan.
  • Year and Date: 20081111-20081114
• [Presentation] Structural studies on the Atg12-Atg5oAtg16 complex essential for autophagy (2008)
  • Author(s): Noda NN, Matsushita M, Obara K, Fujioka Y, Ohsumi Y, Inagaki F.
  • Organizer: Gordon Research Conference on Autophagy in Stress, Development & Disease
  • Place of Presentation: entura, CA, USA.
  • Year and Date: 20080100
• [Presentation] Structure and Interaction of Ubiquitin related Protein Domains:UBA and UBX (2008)
  • Author(s): Tochio H
  • Organizer: Korea-Japan symposium on Biological NMR
  • Place of Presentation: Seoul National University, Seoul, Korea
  • Year and Date: 2008-04-25
• [Presentation] ユビキチンリガーゼgp78とE2の相互作用のNMR解析 (2007)
  • Author(s): 武本映美
  • Organizer: 平成19年度日本薬学会東海支部会例会
  • Place of Presentation: 岐阜
  • Year and Date: 2007-12-08
• [Presentation] 20SプロテアソームのアッセンブリーシャペロンPAC3の結晶構造 (2007)
  • Author(s): 岡本健太
  • Organizer: 第7回日本蛋白質科学会年会
  • Place of Presentation: 仙台
  • Year and Date: 2007-05-26
• [Presentation] NMR法を用いたHOIL-1LのUblドメインの立体構造解析 (2007)
  • Author(s): 三村俊介
  • Organizer: 日本薬学会第127年会
  • Place of Presentation: 富山
  • Year and Date: 2007-03-30
• [Remarks] ホームページ等
  • URL: http://www.rinshoken.or.jp/ER/PRBP/index.html