Elucidation of structural basis for molecular recognition and supramolecular complex formation of intracellular lectins involved in post-endoplasmic reticulum quality control

2011 Fiscal Year Final Research Report

• Project/Area Number: 21370050
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Structural biochemistry
• Research Institution: National Institutes of Natural Sciences Okazaki Research Facilities
• Principal Investigator: KATO Koichi 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 岡崎統合バイオサイエンスセンター, 教授 (20211849)
• Co-Investigator(Kenkyū-buntansha): YAMAGUCHI Takumi 分子科学研究所, 生命・錯体分子科学研究領域, 助教 (60522430) ; KAMIYA Yukiko 大学共同利用機関法人自然科学研究機構(岡崎共通研究施設), 岡崎統合バイオサイエンスセンター, 特任助教 (00527947)
• Co-Investigator(Renkei-kenkyūsha): MIZUSHIMA Tsunehiro 名古屋市立大学, 大学院・薬学研究科, 准教授 (90362269) ; SATO Tadashi 名古屋市立大学, 大学院・薬学研究科, 准教授 (80532100)
• Project Period (FY): 2009 – 2011
• Keywords: 品質管理 / 糖鎖 / レクチン / NMR / 結晶構造解析

Research Abstract

In cells, the carbohydrate moieties serve as tags for the quality control of glycoproteins through interactions with a variety of lectins. To elucidate the mechanisms underlying the glycoprotein quality control by the lectins that cycle between the endoplasmic reticulum and the Golgi, we provided the structural basis for their molecular recognition and complex formation by structural biological approaches such as X-ray crystallography. Furthermore, we successfully developed novel NMR methods for detailed analyses of conformational dynamics of the carbohydrate chains involved in this system.

Research Products

• [Journal Article] Application of paramagnetic NMR-validated molecular dynamics simulation to the analysis of a conformational ensemble of a branched oligosaccharide (2012)
  • Author(s): Y. Zhang, S. Yamamoto, T. Yamaguchi and K. Kato
  • Journal Title: Molecules Volume: 17 Pages: 6658-6671
  • Peer Reviewed
• [Journal Article] A non-canonical UBA-UBL interaction forms the linear-ubiquitin-chain assembly complex (2012)
  • Author(s): H. Yagi, K. Ishimoto, T. Hiromoto, H. Fujita, T. Mizushima, Y. Uekusa, M. Yagi-Utsumi, E. Kurimoto, M. Noda, S. Uchiyama, F. Tokunaga, K. Iwai and K. Kato
  • Journal Title: EMBO reports Volume: 13 Pages: 462-468
  • Peer Reviewed
• [Journal Article] Lanthanide-assisted NMR evaluation of a dynamic ensemble of oligosaccharide conformations (2012)
  • Author(s): S. Yamamoto, Y. Zhang, T. Yamaguchi, T. Kameda and K. Kato
  • Journal Title: Chem. Commun Volume: 48 Pages: 4752-4754
  • Peer Reviewed
• [Journal Article] NMR characterization of the interaction between the PUB domain of peptide : N-glycanase and ubiquitin-like domain of HR23 (2012)
  • Author(s): Y. Kamiya, Y. Uekusa, A. Sumiyoshi, H. Sasakawa, T. Hirao, T. Suzuki and K. Kato
  • Journal Title: FEBS Lett Volume: 586 Pages: 1141-1146
  • Peer Reviewed
• [Journal Article] Development and application of multidimensional HPLC mapping method for O-linked oligosaccharides (2011)
  • Author(s): H. Yagi, E. Ohno, S. Kondo, A. Yoshida and K. Kato
  • Journal Title: Biomolecules Volume: 1 Pages: 48-62
  • Peer Reviewed
• [Journal Article] Conformational dynamics of wild-type Lys-48-linked diubiquitin in solution (2011)
  • Author(s): T. Hirano, O. Serve, M. Yagi-Utsumi, E. Takemoto, T. Hiromoto, T. Satoh, T. Mizushima and K. Kato
  • Journal Title: J. Biol. Chem. Volume: 236 Pages: 37496-37502
  • Peer Reviewed
• [Journal Article] Kinetic asymmetry of subunit exchange of homooligomeric protein as revealed by deuteration-assisted small-angle neutron scattering (2011)
  • Author(s): M. Sugiyama, E. Kurimoto, H. Yagi, K. Mori, T. Fukunaga, M. Hirai, G. Zaccai and K. Kato
  • Journal Title: Biophys. J. Volume: 101 Pages: 2037-2042
  • Peer Reviewed
• [Journal Article] Overexpression of a homogeneous oligosaccharide with^<13> C labeling by genetically engineered yeast strain (2011)
  • Author(s): Y. Kamiya, S. Yamamoto, Y. Chiba, Y. Jigami and K. Kato
  • Journal Title: J. Biomol. NMR Volume: 50 Pages: 397-401
  • Peer Reviewed
• [Journal Article] Paramagnetic Lanthanide tagging for NMR conformational analyses of N-linked oligosaccharides (2011)
  • Author(s): S, Yamamoto, T. Yamaguchi, M. Erdelyi, C. Griesinger and K. Kato
  • Journal Title: Chem. Eur. J Volume: 17 Pages: 9280-9282
  • Peer Reviewed
• [Journal Article] Structural and molecular basis of carbohydrate. protein interaction systems as potential therapeutic targets (2011)
  • Author(s): Y. Kamiya, M. Yagi-Utsumi, H. Yagi and K. Kato
  • Journal Title: Curr. Pharm. Des. Volume: 17 Pages: 1672-1684
  • Peer Reviewed
• [Journal Article] Crystal structures of human secretory proteins ZG16p and ZG16b reveal a Jacalin-relatedβ-prism fold (2011)
  • Author(s): M. Kanagawa, T. Satoh, A. Ikeda, Y. Nakano, H. Yagi, K. Kato, K. Kojima-Aikawa and Y. Yamaguchi
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 404 Pages: 210-205
  • Peer Reviewed
• [Journal Article] Dynamics and interactions of glycoconjugates probed by stable-isotope-assisted NMR spectroscopy (2010)
  • Author(s): Y. Yamaguchi and K. Kato
  • Journal Title: Methods in Enzymology Volume: 478 Pages: 305-322
  • Peer Reviewed
• [Journal Article] Stable-isotope-assisted NMR approaches to glycoproteins using immunoglobulin G as a model system (2010)
  • Author(s): K. Kato, Y. Yamaguchi and Y. Arata
  • Journal Title: Progress in Nuclear Magnetic Resonance Spectroscopy Volume: 56 Pages: 346-359
  • Peer Reviewed
• [Journal Article] Mannose 6-phosphate receptor homology domain-containing lectins in mammalian endoplasmic reticulum-associated degradation (2010)
  • Author(s): N. Hosokawa, Y. Kamiya and K. Kato
  • Journal Title: Methods in Enzymology Volume: 480 Pages: 181-197
  • Peer Reviewed
• [Journal Article] The role of MRH domain-containing lectins in ERAD (2010)
  • Author(s): N. Hosokawa, Y. Kamiya and K. Kato
  • Journal Title: Glycobiology Volume: 20 Pages: 651-660
  • Peer Reviewed
• [Journal Article] Crystal structure of cyclic Lys48-linked tetraubiquitin (2010)
  • Author(s): T. Satoh, E. Sakata, S. Yamamoto, Y. Yamaguchi, A. Sumiyoshi, S. Wakatsuki and K. Kato
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 400 Pages: 329-333
  • Peer Reviewed
• [Journal Article] Redox-dependent domain rearrangement of protein disulfide isomerase from a thermophilic fungus (2010)
  • Author(s): M. Nakasako, A. Maeno, E. Kurimoto, T. Harada, Y. Yamaguchi, T. Oka, Y. Takayama, A. Iwata and K. Kato
  • Journal Title: Biochemistry Volume: 49 Pages: 6953-6962
  • Peer Reviewed
• [Journal Article] Mutational deglycosylation of the Fc portion of immunoglobulin G causes O-sulfation of tyrosine adjacently preceding the originally glycosylated site (2010)
  • Author(s): K. Masuda, Y. Yamaguchi, N. Takahashi, R. Jefferis and K. Kato
  • Journal Title: FEBS Lett. Volume: 584 Pages: 3474-3479
  • Peer Reviewed
• [Journal Article] EDEM1 accelerates the trimming ofα1, 2-linked mannose on the C branch of N-glycans (2010)
  • Author(s): N. Hosokawa, L. O. Tremblay, B. Sleno, Y. Kamiya, I. Wada, K. Nagata, K. Kato and A. Herscovics
  • Journal Title: Glycobiology Volume: 20 Pages: 567-575
  • Peer Reviewed
• [Journal Article] Solution structure and dynamics of mouse ARMET (2010)
  • Author(s): J. Hoseki, H. Sasakawa, Y. Yamaguchi, M. Maeda, H. Kubota, K. Kato
  • Journal Title: FEBS Lett. Volume: 584 Pages: 1536-1542
  • Peer Reviewed
• [Journal Article] Structural basis for the cooperative interplay between the two causative gene products of combined factor V and factor VIII deficiency (2010)
  • Author(s): M. Nishio, Y. Kamiya, T. Mizushima, S. Wakatsuki, H. Sasakawa, K. Yamamoto, S. Uchiyama, M. Noda, A. R. McKay, K. Fukui, H.-P. Hauri and K. Kato
  • Journal Title: Proc. Natl. Acad. Sci. U. S. A. Volume: 107 Pages: 4034-4039
  • Peer Reviewed
• [Journal Article] Improved secretion of molecular chaperone-assisted human IgG in silkworm, and no alterations in their N-linked glycan structures (2010)
  • Author(s): T. Dojima, T. Nishina, T. Kato, T. Uno, H. Yagi, K. Kato, H. Ueda and E. Y. Park
  • Journal Title: Biotechnology Progress Volume: 26 Pages: 232-238
  • Peer Reviewed
• [Journal Article] Redox-dependent domain rearrangement of protein disulfide isomerase coupled with exposure of its substrate-binding hydrophobic surface (2010)
  • Author(s): O. Serve, Y. Kamiya, A. Maeno, M. Nakano, C. Murakami, H. Sasakawa, Y. Yamaguchi, T. Harada, E. Kurimoto, M. Utsumi-Yagi, T. Iguchi, K. Inaba, J. Kikuchi, O. Asami, T. Kajino, T. Oka, M. Nakasako and K. Kato
  • Journal Title: J. Mol. Biol. Volume: 396 Pages: 361-374
  • Peer Reviewed
• [Journal Article] N-Glycosylation profiling of turtle egg yolk : expression of galabiose structure (2010)
  • Author(s): H. Yagi, M. Yamamoto, S.-Y. Yu, N. Takahashi, K.-H. Khoo, Y. C. Lee and K. Kato
  • Journal Title: Carbohyd. Res. Volume: 345 Pages: 442-448
  • Peer Reviewed
• [Journal Article] Crystal structure of UbcH5b～ ubiquitin intermediate : Insight into the formation of the self-assembled E2～ Ub conjugates (2010)
  • Author(s): E. Sakata, T. Satoh, S. Yamamoto, Y. Yamaguchi, M. Yagi-Utsumi, E. Kurimoto, K. Tanaka, S. Wakatsuki and K. Kato
  • Journal Title: Structure Volume: 18 Pages: 138-147
  • Peer Reviewed
• [Journal Article] Multidimensional HPLC mapping method for the structural analysis of anionic N-glycans (2009)
  • Author(s): H. Yagi and K. Kato
  • Journal Title: Trends Glycosci. Glycotech Volume: 21 Pages: 96-104
  • Peer Reviewed
• [Journal Article] Silkworm expression and sugar profiling of human immune cell surface receptor, KIR2DL1 (2009)
  • Author(s): K. Sasaki, M. Kajikawa, K. Kuroki, T. Motohashi, T. Shimojima, E. Y. Park, S. Kondo, H. Yagi, K. Kato and K. Maenaka
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 387 Pages: 575-580
  • Peer Reviewed
• [Journal Article] Human OS-9, a lectin required for glycoprotein endoplasmic reticulum-associated degradation, recognizes mannose-trimmed N-glycans (2009)
  • Author(s): N. Hosokawa, Y. Kamiya, D. Kamiya, K. Kato and K. Nagata
  • Journal Title: J. Biol. Chem. Volume: 284 Pages: 17061-17068
  • Peer Reviewed
• [Journal Article] Analysis of N-glycans in embryonated chicken egg chorioallantoic and amniotic cells responsible for binding and adaptation of human and avian influenza viruses (2009)
  • Author(s): N. Sriwilaijaroen, S. Kondo, H. Yagi, P. Wilairat, H. Hiramatsu, M. Ito, Y. Ito, K. Kato and Y. Suzuki
  • Journal Title: Glycoconjugate J. Volume: 26 Pages: 433-443
  • Peer Reviewed
• [Presentation] Application of paramagnetic NMR to analyses of conformations and dynamics of oligosaccharides (2011)
  • Author(s): S. Yamamoto, T. Yamaguchi, Y. Zhang, M. Erdelyi, C. Griesinger and K. Kato
  • Organizer: The International Symposium on Nuclear Magnetic Resonance 2011(ISNMR 2011)
  • Place of Presentation: 大さん橋ホール(神奈川)
  • Year and Date: 2011-11-16
• [Presentation] Development of metabolic isotope-labeling techniques for NMR spectroscopic analyses of highmannose-type oligosaccharides (2011)
  • Author(s): Y. Kamiya, S. Yamamoto, Y. Chiba, Y. Jigami and K. Kato
  • Organizer: The International Symposium on Nuclear Magnetic Resonance 2011(ISNMR 2011)
  • Place of Presentation: 大さん橋ホール(神奈川)
  • Year and Date: 2011-11-16
• [Presentation] Structural and Molecular Basis of Carbohydrate-Protein Interaction Systems as Potential Therapeutic Targets (2011)
  • Author(s): K. Kato
  • Organizer: 3^<rd> Asian Communications of Glycobiology and Glycotechnology(ACGG 3^<rd> Conference), Shanghai Institute of Organic Chemistry
  • Place of Presentation: Shanghai, China
  • Year and Date: 2011-10-27
• [Presentation] Structural views of functional and pathological roies of sugar chains (2011)
  • Author(s): K. Kato
  • Organizer: 第71回岡崎コンファレンス「糖鎖分子科学の新たな展望」,岡崎コンファレンスセンター
  • Place of Presentation: 愛知
  • Year and Date: 2011-10-12
• [Presentation] NMR analyses of carbohydrate-protein interaction systems as potential therapeutic targets (2011)
  • Author(s): K. Kato, H. Yagi, T. Yamaguchi, S. Yamamoto, Y. Kamiya and M. Yagi-Utsumi
  • Organizer: Glycobiology Japan-Netherland Joint Seminar 2011
  • Place of Presentation: 名古屋大学(愛知)
  • Year and Date: 2011-10-10
• [Presentation] A systematic approach for structural glycoproteomics (2011)
  • Author(s): K. Kato
  • Organizer: The 23rd Annual Meeting of the Korean Society for Molecular and Cellular Biology
  • Place of Presentation: COEX(Seoul, Korea)
  • Year and Date: 2011-10-07
• [Presentation] Structural and molecular basis of carbohydrate-protein interaction systems as potential therapeutic targets (2011)
  • Author(s): K. Kato
  • Organizer: 第31回内藤コンファレンス,シャトレーゼガトーキングダムサッポロ
  • Place of Presentation: 北海道
  • Year and Date: 2011-09-15
• [Presentation] A systematic approach to structural glycobiology (2011)
  • Author(s): K. Kato, H. Yagi, Y. Kamiya, M. Nishio, T. Yamaguchi, S. Yamamoto, M. Yagi-Utsumi and T. Mizushima
  • Organizer: 3rd Korea-Japan Seminar on Biomolecular Sciences-Experiments and Simulations
  • Place of Presentation: LOTTE Hotel(Jeju, Korea)
  • Year and Date: 2011-02-27
• [Presentation] Structural views of the ubiquitin-proteasome system (2010)
  • Author(s): K. Kato and T. Mizushima
  • Organizer: The 2010 International Chemical Congress of Pacific Basin Societies(PACIFICHEM 2010)
  • Place of Presentation: ハワイコンベンションセンター(Honolulu, U. S. A.)
  • Year and Date: 2010-12-18
• [Presentation] Structural and functional glycomics based on HPLC database, sugar library, and NMR spectroscopy (2010)
  • Author(s): K. Kato
  • Organizer: BIT Life Sciences 8th Annual Congress of International Drug Discovery Science and Technology(IDDST)
  • Place of Presentation: Beijin International Convention Center(Beijin, China)
  • Year and Date: 2010-10-24
• [Presentation] NMR characterization of conformations, dynamics, and interactions of glycoconjugates (2010)
  • Author(s): K. Kato
  • Organizer: The 25th International Carbohydrate Symposium
  • Place of Presentation: 幕張メッセ(千葉)
  • Year and Date: 2010-08-03
• [Presentation] A systematic approaches of structural glycobiology based on NMR and sugar library (2010)
  • Author(s): K. Kato
  • Organizer: International Workshop on Glycan Structure Analysis of Therapeutic Recombinant Glycoproteins
  • Place of Presentation: Cardinal Kim Sou Hwan International Sacred Heart Convention Center(Bucheon, Korea)
  • Year and Date: 2010-07-23
• [Presentation] A systematic approach to NMR-based structural glycobiology (2010)
  • Author(s): K. Kato, Y. Kamiya and Y. Yamaguchi
  • Organizer: Joint EUROMAR 2010 and 17^<th> ISMAR Conference, Palazzo dei Congressi and Palazzo degli Affari
  • Place of Presentation: Firenze, Italy
  • Year and Date: 2010-07-06
• [Presentation] Structural basis for the functional mechanisms of the proteins involved in the ubiquitin-proteasome system (2009)
  • Author(s): K. Kato
  • Organizer: 2nd Japan-Korea Seminar on Biomolecular Sciences. Experiments and Simulations
  • Place of Presentation: 名古屋大学(愛知)
  • Year and Date: 2009-12-23
• [Presentation] Stable-isotope-assisted NMR approaches to structural glycomics (2009)
  • Author(s): K. Kato
  • Organizer: 20^<th> International Symposium on Glycoconjugates
  • Place of Presentation: Caribe Hilton(Puerto Rico)
  • Year and Date: 2009-11-30
• [Presentation] Structural Glycobiology by NMR and Sugar Library Approaches (2009)
  • Author(s): K. Kato
  • Organizer: 3^<rd> Asia-Pacific NMR symposium
  • Place of Presentation: Ramada Plaza Jeju Hotel(Jeju, Korea)
  • Year and Date: 2009-10-27
• [Book] Protein Folding (2011)
  • Author(s): O. Serve, Y. Kamiya and K. Kato
  • Total Pages: 489-500
  • Publisher: NOVA Science Publishers
• [Book] Glycobiology Research Trends (2009)
  • Author(s): Y. Kamiya, D. Kamiya, R. Urade, T. Suzuki and K. Kato
  • Total Pages: 27-40
  • Publisher: NOVA Science Publishers