Personnel Information

写真a

NUMOTO Nobutaka


Job title

Associate Professor

Birth date

1975

Graduating School 【 display / non-display

  • Kyoto University, Faculty of Science, 1999.03, Graduated

Graduate School 【 display / non-display

  • Kyoto University, Graduate School, Division of Natural Science, Master's Course, 2001.03, Completed

  • Kyoto University, Graduate School, Division of Natural Science, Doctor's Course, 2004.03, Accomplished credits for doctoral program

Degree 【 display / non-display

  • Ph.D., Kyoto University

Campus Career 【 display / non-display

  • 2012.10
    -
    2021.05
    Tokyo Medical and Dental University, Medical Research Institute, Advanced Molecular Medicine, Structural Biology, Assistant Professor
  • 2012.10
    -
    Now
    Tokyo Medical and Dental University, Graduate School of Medical and Dental Sciences, Life Science and Technology, Life Science and Technology, Structural Biology, Assistant Professor
  • 2021.06
    -
    2022.04
    Tokyo Medical and Dental University, Medical Research Institute, Advanced Molecular Medicine, Structural Biology, Associate Professor
  • 2022.05
    -
    Now
    Tokyo Medical and Dental University, Medical Research Institute, a, Department of Structural Biology, Associate Professor

Research Areas 【 display / non-display

  • Structural biochemistry

 

Published Papers & Misc 【 display / non-display

  1. Nobutaka Numoto, Seiko Onoda, Yoshiaki Kawano, Hideo Okumura, Seiki Baba, Yoshihiro Fukumori, Kunio Miki, Nobutoshi Ito. Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery. Biophys Physicobiol. 2022.05; 19 1-10. ( PubMed, DOI )

  2. Yoshihara Ayana, Kawasaki Haru, Masuno Hiroyuki, Takada Koki, Numoto Nobutaka, Ito Nobutoshi, Hirata Naoya, Kanda Yasunari, Ishizawa Michiyasu, Makishima Makoto, Kagechika Hiroyuki, Tanatani Aya. Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists Biomolecules. 2022.01; 12 (1): 130. ( PubMed, DOI )

  3. Fujioka Toshifumi, Numoto Nobutaka, Akama Hiroyuki, Shilpa Kola, Oka Michiko, Roy Prodip K., Krishna Yarkali, Ito Nobutoshi, Baker David, Oda Masayuki, Tanaka Fujie. Varying the Directionality of Protein Catalysts for Aldol and Retro-Aldol Reactions ChemBioChem. 2022.01; 23 (2): e202100435. ( PubMed, DOI )

  4. Numoto Nobutaka, Kawano Yoshiaki, Okumura Hideo, Baba Seiki, Fukumori Yoshihiro, Miki Kunio, Ito Nobutoshi. Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state IUCrJ. 2021.11; 8 (Pt 6): 954-962. ( PubMed, DOI )

  5. Miho Emori, Nobutaka Numoto, Akane Senga, Gert-Jan Bekker, Narutoshi Kamiya, Yuma Kobayashi, Nobutoshi Ito, Fusako Kawai, Masayuki Oda. Structural basis of mutants of PET-degrading enzyme from Saccharomonospora viridis AHK190 with high activity and thermal stability. Proteins. 2021.05; 89 (5): 502-511. ( PubMed, DOI )

  6. Momoka Iiyama, Nobutaka Numoto, Shuhei Ogawa, Masataka Kuroda, Hisayuki Morii, Ryo Abe, Nobutoshi Ito, Masayuki Oda. Molecular interactions of the CTLA-4 cytoplasmic region with the phosphoinositide 3-kinase SH2 domains. Mol Immunol. 2021.03; 131 51-59. ( PubMed, DOI )

  7. Akane Senga, Nobutaka Numoto, Mitsuaki Yamashita, Akira Iida, Nobutoshi Ito, Fusako Kawai, Masayuki Oda. Multiple structural states of Ca2+-regulated PET hydrolase, Cut190, and its correlation with activity and stability. J Biochem. 2021.03; 169 (2): 207-213. ( PubMed, DOI )

  8. Masayuki Oda, Nobutaka Numoto, Gert-Jan Bekker, Narutoshi Kamiya, Fusako Kawai. Cutinases from thermophilic bacteria (actinomycetes): From identification to functional and structural characterization. Methods Enzymol. 2021.02; 648 159-185. ( PubMed, DOI )

  9. Alborzian Deh Sheikh A, Gomaa S, Li X, Routledge M, Saigoh K, Numoto N, Angata T, Hitomi Y, Takematsu H, Tsuiji M, Ito N, Kusunoki S, Tsubata T. A Guillain-Barré syndrome-associated SIGLEC10 rare variant impairs its recognition of gangliosides. Journal of autoimmunity. 2021.01; 116 102571. ( PubMed, DOI )

  10. Numoto N, Kamiya N, Kawai F, Oda M. Crystal Structures of Polyethylene Terephthalate-Degrading Enzyme Cut190 in Substrate-Bound States Reveal the Enzymatic Reaction Cycle Accelerated by Calcium Ion ACS Symposium Series "Green Polymer Chemistry and Sustainability.". 2021; ( DOI )

  11. Sasaki H, Masuno H, Kawasaki H, Yoshihara A, Numoto N, Ito N, Ishida H, Yamamoto K, Hirata N, Kanda Y, Kawachi E, Kagechika H, Tanatani A. Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists. Journal of medicinal chemistry. 2020.12; ( PubMed, DOI )

  12. Akihiro Nishiguchi, Nobutaka Numoto, Nobutoshi Ito, Takachika Azuma, Masayuki Oda. Three-dimensional structure of a high affinity anti-(4-hydroxy-3-nitrophenyl)acetyl antibody possessing a glycine residue at position 95 of the heavy chain. Mol. Immunol.. 2019.10; 114 545-552. ( PubMed, DOI )

  13. Yuhi Hosoe, Nobutaka Numoto, Satomi Inaba, Shuhei Ogawa, Hisayuki Morii, Ryo Abe, Nobutoshi Ito, Masayuki Oda. Structural and functional properties of Grb2 SH2 dimer in CD28 binding. Biophys Physicobiol. 2019.02; 16 80-88. ( PubMed, DOI )

  14. Yurina Miyashita, Nobutaka Numoto, Sundaram Arulmozhiraja, Shogo Nakano, Naoya Matsuo, Kanade Shimizu, Osamu Shibahara, Michiko Fujihara, Hiroki Kakuta, Sohei Ito, Teikichi Ikura, Nobutoshi Ito, Hiroaki Tokiwa. Dual conformation of the ligand induces the partial agonistic activity of retinoid X receptor α (RXRα). FEBS Lett.. 2019.01; 593 (2): 242-250. ( PubMed, DOI )

  15. Numoto N, Kamiya N, Bekker GJ, Yamagami Y, Inaba S, Ishii K, Uchiyama S, Kawai F, Ito N, Oda M. Structural Dynamics of PET-degrading Cutinase-like Enzyme from Saccharomonospora viridis AHK190 in Substrate-bound States Elucidates Ca2+ Driven Catalytic Cycle. Biochemistry. 2018.09; 57 (36): 5289-5300. ( PubMed, DOI )

  16. Rocio Otero, Michiyasu Ishizawa, Nobutaka Numoto, Teikichi Ikura, Nobutoshi Ito, Hiroaki Tokiwa, Antonio Mouriño, Makoto Makishima, Sachiko Yamada. 25 S-Adamantyl-23-yne-26,27-dinor-1α,25-dihydroxyvitamin D3: Synthesis, Tissue Selective Biological Activities, and X-ray Crystal Structural Analysis of Its Vitamin D Receptor Complex. J. Med. Chem.. 2018.08; 61 (15): 6658-6673. ( PubMed, DOI )

  17. Naoko Matsubara, Akihiro Imamura, Tatsuya Yonemizu, Chizuru Akatsu, Hongrui Yang, Akiharu Ueki, Natsuki Watanabe, Hajjaj Abdu-Allah, Nobutaka Numoto, Hiromu Takematsu, Shinobu Kitazume, Thomas F Tedder, Jamey D Marth, Nobutoshi Ito, Hiromune Ando, Hideharu Ishida, Makoto Kiso, Takeshi Tsubata. CD22-Binding Synthetic Sialosides Regulate B Lymphocyte Proliferation Through CD22 Ligand-Dependent and Independent Pathways, and Enhance Antibody Production in Mice. Front Immunol. 2018.04; 9 820. ( PubMed, DOI )

  18. Satomi Inaba, Nobutaka Numoto, Shuhei Ogawa, Hisayuki Morii, Teikichi Ikura, Ryo Abe, Nobutoshi Ito, Masayuki Oda. Crystal Structures and Thermodynamic Analysis Reveal Distinct Mechanisms of CD28 Phosphopeptide Binding to the Src Homology 2 (SH2) Domains of Three Adaptor Proteins. J. Biol. Chem.. 2017.01; 292 (3): 1052-1060. ( PubMed, DOI )

  19. Chizuru Akatsu, Kenro Shinagawa, Nobutaka Numoto, Zhihong Liu, Ayse Konuskan Ucar, Mohammad Aslam, Shirly Phoon, Takahiro Adachi, Koji Furukawa, Nobutoshi Ito, Takeshi Tsubata. CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP. J. Exp. Med.. 2016.11; 213 (12): 2691-2706. ( PubMed, DOI )

  20. Akira Nakamura, Jun Ohtsuka, Tatsuki Kashiwagi, Nobutaka Numoto, Noriyuki Hirota, Takahiro Ode, Hidehiko Okada, Koji Nagata, Motosuke Kiyohara, Ei-Ichiro Suzuki, Akiko Kita, Hitoshi Wada, Masaru Tanokura. In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth. Sci Rep. 2016.02; 6 22127. ( PubMed, DOI )

  21. Manjiri R Kulkarni, Nobutaka Numoto, Nobutoshi Ito, Yutaka Kuroda. Modeling and experimental assessment of a buried Leu-Ile mutation in dengue envelope domain III. Biochem. Biophys. Res. Commun.. 2016.02; 471 (1): 163-168. ( PubMed, DOI )

  22. Manjiri R Kulkarni, Monirul M Islam, Nobutaka Numoto, Montasir Elahi, Mamunur R Mahib, Nobutoshi Ito, Yutaka Kuroda. Structural and biophysical analysis of sero-specific immune responses using epitope grafted Dengue ED3 mutants. Biochim. Biophys. Acta. 2015.10; 1854 (10 Pt A): 1438-1443. ( PubMed, DOI )

  23. Nobutaka Numoto, Taro Nakagawa, Ryota Ohara, Tomoyo Hasegawa, Akiko Kita, Takao Yoshida, Tadashi Maruyama, Kiyohiro Imai, Yoshihiro Fukumori, Kunio Miki. The structure of a deoxygenated 400 kDa haemoglobin reveals ternary- and quaternary-structural changes of giant haemoglobins. Acta Crystallogr. D Biol. Crystallogr.. 2014.07; 70 (Pt 7): 1823-1831. ( PubMed, DOI )

  24. Yumemi Nagamatsu, Kazuki Takeda, Takeshi Kuranaga, Nobutaka Numoto, Kunio Miki. Origin of asymmetry at the intersubunit interfaces of V1-ATPase from Thermus thermophilus. J. Mol. Biol.. 2013.08; 425 (15): 2699-2708. ( PubMed, DOI )

  25. Nobutaka Numoto, Ken-ichi Shimizu, Kazuya Matsumoto, Kunio Miki, Akiko Kita. Observation of the orientation of membrane protein crystals grown in high magnetic force fields. J. Cryst. Growth. 2013; 367 53-56.

  26. Nobutaka Numoto, Akiko Kita, Noriko Fujii, Kunio Miki. A P39R mutation at the N-terminal domain of human αB-crystallin regulates its oligomeric state and chaperone-like activity. Biochem. Biophys. Res. Commun.. 2012.08; 425 (3): 601-606. ( PubMed, DOI )

  27. Nobutaka Numoto, Yu Hasegawa, Kazuki Takeda, Kunio Miki. Inter-subunit interaction and quaternary rearrangement defined by the central stalk of prokaryotic V1-ATPase. EMBO Rep.. 2009.11; 10 (11): 1228-1234. ( PubMed, DOI )

  28. Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Yuichi Sasayama, Yoshihiro Fukumori, Kunio Miki. Structure of the partially unliganded met state of 400 kDa hemoglobin: insights into ligand-induced structural changes of giant hemoglobins. Proteins. 2008.10; 73 (1): 113-125. ( PubMed, DOI )

  29. Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Yuichi Sasayama, Yoshihiro Fukumori, Kunio Miki. Structural basis for the heterotropic and homotropic interactions of invertebrate giant hemoglobin. Biochemistry. 2008.10; 47 (43): 11231-11238. ( PubMed, DOI )

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Conference Activities & Talks 【 display / non-display

  1. Xibin Quan, Nobutaka Numoto, Takeshi Tsubata, Nobutoshi Ito. Structure analysis of human B cell inhibitory co-receptor CD72. The 60th Annual Meeting of the Biophysical Society of Japan 2022.09.28 Hakodate

  2. Nobutaka Numoto, Narutoshi Kamiya, Masayuki Oda. Improvement of thermostability and activity of PET-degrading enzyme Cut190 towards a detailed understanding and application of the enzymatic reaction mechanism. ACS Fall 2022 2022.08.25 Chicago (USA)

  3. Nobutaka Numoto, Kunio Hirata, Chizuru Akatsu, Takeshi Tsubata, Nobutoshi Ito. Molecular mechanism of self-antigen recognition by the ligand binding domain of B cell inhibitory co-receptor CD72. 25th Congress and General Assembly of the International Union of Crystallography 2021.08.20 Prague / on-line hybrid meeting

  4. Alborzian Deh Sheikh A., Li X., Gomaa S., Routledge M., Numoto N., Ito N., Kusunoki S., Tsubata T.. Guillain-Barré syndrome-associated SIGLEC10 rare variant impairs its recognition of gangliosides. 第85回日本インターフェロン・サイトカイン学会学術集会 2021.05.21

  5. Daisuke Imai, Nobutaka Numoto, Sundaram Arulmozhiraja, Shogo Masuda, Hiroki Kakuta, Hiroaki Tokiwa, Nobutoshi Ito. Structural analysis of NEt-3IB/NEt-4IB-bound Retinoid X Receptor α. 16th Conference of the Asian Crystallographic Association 2019.12.18 Singapore

  6. 宮下由里奈, 沼本修孝, ラジャサンダラム, 中野祥吾, 松尾直也, 清水奏, 芝原理, 藤原美智子, 加来田博貴, 伊藤創平, 伊倉貞吉, 伊藤暢聡, 常盤広明. RXRαリガンド結合ドメイン四量体と新規合成パーシャルアゴニストとの複合体結晶構造. 第56回日本生物物理学会年会 2018.09.15

  7. Nobutaka Numoto. Molecular recognition mechanism of proteins revealed by X-ray crystallography. 2018.05.18 Okinawa Institute of Science and Technology Graduate University

  8. Kanade Shimizu, Yurina Miyashita, Yuta Yamamoto, Naoya Matsuo, Shogo Nakano, Sohei Ito, Nobutaka Numoto, Nobutoshi Ito, Hiroki Kakuta, Hiroaki Tokiwa. What is the origin of partial agonist activity of CBt-PMN for hRXRα?. Experimental biology 2018 2018.04.24 USA

  9. Yurina Miyashita, Naoya Matsuo, Yuta Yamamoto, Shogo Nakano, Sohei Ito, Nobutaka Numoto, Teikichi Ikura, Nobutoshi Ito, Motohiro Sekiya, Hitoshi Shimano, and Hiroaki Tokiwa. Computational design and molecular mechanism in oligomerization of C-terminal binding protein 2. Experimental biology 2018 2018.04.24 USA

  10. Takeshi Kawabata, Masayuki Oda, Satomi Inaba, Nobutaka Numoto, Fusako Kawai. Structural and mutational analysis of PET-hydolyzing enzyme, Cut190, based on the 3D docking structure with model compounds of PET. 254th American Chemical Society National Meeting & Exposition 2017.08.20 Washington, DC, USA

  11. 稲葉理美, 沼本修孝, 小川修平, 森井尚之, 伊倉貞吉, 安部良, 伊藤暢聡, 織田昌幸. CD28とSH2ドメインとの相互作用における構造熱力学的解析. 第54回日本生物物理学会年会 2016.11 茨城

  12. Chizuru Akatsu,Kenro Shinagawa, Nobutaka Numoto, Zhihong Liu, Mohommad Aslam, Nobutoshi Ito, Takeshi Tsubata. B cells reactive to Sm/RNP, a lupus-related self-antigen. 12th International Conference on Protein Phosphatase (ICPP12) 2016.10.28 OSAKA

  13. Inaba S., Numoto N., Morii H., Ikura T., Abe R., Ito N., Oda M.. Structural and thermodynamic analysis of co-stimulation receptor CD28 phosphopeptide interactions with Grb2, Gads, and PI3-kinese SH2 domains. The 29th Annual Symposium of The Protein Society 2015.07 Palau de Congressos de Barcelona, Barcelona (Spain)

  14. Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Nobutoshi Ito, Yoshihiro Fukumori, Kunio Miki. 巨大ヘモグロビン結晶内での oxy 型から deoxy 型への移行. 第52回日本生物物理学会年会 2014.09 札幌

  15. Kenro Shinagawa, Nobutaka Numoto, Takeshi Tsubata, Nobutoshi Ito. B 細胞共受容体 CD72 の C 型レクチン様ドメインの X 線結晶構造解析. 第52回日本生物物理学会年会 2014.09 札幌

  16. Nobutaka Numoto, Taro Nakagawa, Akiko Kita, Nobutoshi Ito, Yoshihiro Fukumori,Kunio Miki. Partial oxygen-dissociation of crystalline giant hemoglobin. Twenty-Third Congress and General Assembly of the International Union of Crystallography 2014.08 Montreal (Canada)

  17. Manjiri Rabindoura Kurukaruni、Montasiru Elahi、Monirul M Islamu、 Nobutoshi Ito、 Nobutaka Numoto、Yutaka Kuroda. Epitope-grafted mutants provide molecular insights into sero-specifc interactions of Dengue's ED3 with its monoclonal antibody. 第14回日本蛋白質科学会年会 2014.06 横浜

  18. 品川健朗,沼本修孝,鍔田武志,伊藤暢聡. CD72の構造解析に向けて. 第51回日本生物物理学会年会 2013.10 京都

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Campus class subject 【 display / non-display

  • Special Lecture on Molecular Structures,2012 - Now

External class subject 【 display / non-display

  • ,Tokyo University of Agriculture and Technology