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Structural and functional analysis of glycosidases from plants that have a novel active center

Research Project

Project/Area Number 26660083
Research Category

Grant-in-Aid for Challenging Exploratory Research

Allocation TypeMulti-year Fund
Research Field Applied biochemistry
Research InstitutionThe University of Tokyo

Principal Investigator

Fushinobu Shinya  東京大学, 大学院農学生命科学研究科(農学部), 教授 (00302589)

Research Collaborator FUJITA Kiyotaka  鹿児島大学, 農学部, 准教授
ISHIWATA Akihiro  理化学研究所, 専任研究員
ITO Yukishige  理化学研究所, 主任研究員
Beckham Gregg T.  米国NREL, 研究員
Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Fiscal Year 2016: ¥1,300,000 (Direct Cost: ¥1,000,000、Indirect Cost: ¥300,000)
Fiscal Year 2015: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000)
Fiscal Year 2014: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
Keywordsグリコシダーゼ / シロイヌナズナ / イネ / β-アラビノオリゴ糖 / 糖質関連酵素
Outline of Final Research Achievements

We initially aimed to study the structure and function of uncharacterized enzyme from plants that belong to DUF1680. Although we examined heterologous expression of the genes from Arabidopsis thaliana and Oryza sativa under various conditions, they did not express or expressed as insoluble aggregates. We determined a novel crystal structure of a GH146 β-L-arabinofuranosidase from plant pathogen, Xanthomonas. The active site of the Xanthomonas enzyme was cysteine, like the case of GH127 enzyme (HypBA1), and the enzyme had a novel carbohydrate-binding module domain.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Research-status Report
  • 2015 Research-status Report
  • 2014 Research-status Report
  • Research Products

    (21 results)

All 2017 2016 2015 2014 Other

All Journal Article (14 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 14 results,  Acknowledgement Compliant: 6 results,  Open Access: 4 results) Presentation (6 results) (of which Invited: 3 results) Remarks (1 results)

  • [Journal Article] Discovery of α-l-arabinopyranosidases from human gut microbiome expands the diversity within glycoside hydrolase family 422017

    • Author(s)
      Viborg Alexander Holm、Katayama Takane、Arakawa Takatoshi、Abou Hachem Maher、Lo Leggio Leila、Kitaoka Motomitsu、Svensson Birte、Fushinobu Shinya
    • Journal Title

      Journal of Biological Chemistry

      Volume: 292 Issue: 51 Pages: 21092-21101

    • DOI

      10.1074/jbc.m117.792598

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Crystal Structure and Substrate Specificity Modification of Acetyl Xylan Esterase from Aspergillus luchuensis2017

    • Author(s)
      Komiya Dai、Hori Akane、Ishida Takuya、Igarashi Kiyohiko、Samejima Masahiro、Koseki Takuya、Fushinobu Shinya
    • Journal Title

      Applied and Environmental Microbiology

      Volume: 83 Issue: 20

    • DOI

      10.1128/aem.01251-17

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The First Crystal Structure of a Family 129 Glycoside Hydrolase from a Probiotic Bacterium Reveals Critical Residues and Metal Co-factors2017

    • Author(s)
      Mayo Sato, Dorothee Liebschner, Yusuke Yamada, Naohiro Matsugaki, Takatoshi Arakawa, Siobhan S. Wills, Mitchell Hattie, Keith A. Stubbs, Tasuku Ito, Toshiya Senda, Hisashi Ashida and Shinya Fushinobu
    • Journal Title

      Journal of Biological Chemistry

      Volume: 292 Issue: 29 Pages: 12126-12138

    • DOI

      10.1074/jbc.m117.777391

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Journal Article] Molecular Insight into Evolution of Symbiosis between Breast-Fed Infants and a Member of the Human Gut Microbiome Bifidobacterium longum2017

    • Author(s)
      Yamada C, Gotoh A, Sakanaka M, Hattie M, Stubbs KA, Katayama-Ikegami A, Hirose J, Kurihara S, Arakawa T, Kitaoka M, Okuda S, Katayama T and Fushinobu S.
    • Journal Title

      Cell Chemical Biology

      Volume: 24 Issue: 4 Pages: 515-524

    • DOI

      10.1016/j.chembiol.2017.03.012

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] The crystal structure of an inverting glycoside hydrolase family 9 exo-β-D-glucosaminidase and the design of glycosynthase2016

    • Author(s)
      Y. Honda, S. Arai, K. Suzuki, M. Kitaoka, and S. Fushinobu
    • Journal Title

      Biochem. J.

      Volume: 473 Issue: 4 Pages: 463-472

    • DOI

      10.1042/bj20150966

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Archaeal Mo-containing glyceraldehyde oxidoreductase isozymes exhibit diverse substrate specificities through unique subunit assemblies2016

    • Author(s)
      T. Wakagi, H. Nishimasu, M. Miyake, and S. Fushinobu
    • Journal Title

      PLOS ONE

      Volume: 11 Issue: 1 Pages: e0147333-e0147333

    • DOI

      10.1371/journal.pone.0147333

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Crystal structure and identification of a key amino acid for glucose tolerance, substrate specificity and transglycosylation activity of metagenomic β-glucosidase Td2F2.2016

    • Author(s)
      Tomohiko Matsuzawa, Toshinori Jo, Taku Uchiyama, Jenny A Manninen, Takatoshi Arakawa, Kentaro Miyazaki, Shinya Fushinobu, Katsuro Yaoi
    • Journal Title

      FEBS Journal

      Volume: - Issue: 12 Pages: 2340-2353

    • DOI

      10.1111/febs.13743

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] rystal structures of archaeal 2-oxoacid:ferredoxin oxidoreductases from Sulfolobus tokodaii2016

    • Author(s)
      Z. Yan, A. Maruyama, T. Arakawa, S. Fushinobu, and T. Wakagi
    • Journal Title

      Sci. Rep.

      Volume: 6 Issue: 1 Pages: 33061-33061

    • DOI

      10.1038/srep33061

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Characterization and crystal structure determination of β-1,2-mannobiose phosphorylase from Listeria innocua2015

    • Author(s)
      T. Tsuda, T. Nihira, K. Chiku, E. Suzuki, T. Arakawa, M. Nishimoto, M. Kitaoka, H. Nakai, and S. Fushinobu
    • Journal Title

      FEBS Lett.

      Volume: 589 Issue: 24PartB Pages: 3816-3821

    • DOI

      10.1016/j.febslet.2015.11.034

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Crystal structure and substrate recognition of cellobionic acid phosphorylase, which plays a key role in oxidative cellulose degradation by microbes2015

    • Author(s)
      Y.-W. Nam, T. Nihira, T. Arakawa, Y. Saito, M. Kitaoka, H. Nakai, and S. Fushinobu
    • Journal Title

      J. BIol. Chem.

      Volume: 290 Issue: 30 Pages: 18281-18292

    • DOI

      10.1074/jbc.m115.664664

    • Related Report
      2015 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Open-close structural change upon ligand binding and two magnesium ions required for the catalysis of N-acetylhexosamine 1-kinase2015

    • Author(s)
      佐藤真与、荒川孝俊、伏信進矢ら
    • Journal Title

      BBA - Proteins Proteom.

      Volume: 1854 Issue: 5 Pages: 333-340

    • DOI

      10.1016/j.bbapap.2015.01.011

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural basis for the 4'-hydroxylation of diclofenac by a microbial cytochrome P450 monooxygenase.2015

    • Author(s)
      L.-H. Xu, H. Ikeda, L. Liu, T. Arakawa, T. Wakagi, H. Shoun, S. Fushinobu
    • Journal Title

      Appl. Microbiol. Biotechnol,

      Volume: 99 Issue: 7 Pages: 3081-3091

    • DOI

      10.1007/s00253-014-6148-y

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Crystal structure of a feruloyl esterase belonging to the tannase family: a disulfide bond near a catalytic triad2014

    • Author(s)
      鈴木健太郎、荒川孝俊、伏信進矢ら
    • Journal Title

      Proteins: Struct. Funct. Bioinform.

      Volume: 82 Issue: 10 Pages: 2857-2867

    • DOI

      10.1002/prot.24649

    • Related Report
      2014 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Structural basis for reversible phosphorolysis and hydrolysis reactions of 2-O-α-glucosylglycerol phosphorylase2014

    • Author(s)
      東原幸起、荒川孝俊、伏信進矢ら
    • Journal Title

      J. Biol. Chem.

      Volume: 289 Issue: 26 Pages: 18067-18075

    • DOI

      10.1074/jbc.m114.573212

    • Related Report
      2014 Research-status Report
    • Peer Reviewed
  • [Presentation] B. longum JCM1217由来GH127 β-L-アラビノフラノシダーゼ (HypBA1)の機能構造解析2017

    • Author(s)
      丸山 瞬、伊藤 佑、藤田 清貴、石渡 明弘、伊藤 幸成、荒川 孝俊、伏信 進矢
    • Organizer
      日本農芸化学会大会
    • Place of Presentation
      京都女子大(京都府 京都市)
    • Year and Date
      2017-03-17
    • Related Report
      2016 Research-status Report
  • [Presentation] Xhanthomonas 属由来β-L-アラビノフラノシダーゼの機能・構造解析2017

    • Author(s)
      澤野孝太、丸山瞬、荒川孝俊、石渡明弘、中村正幸、伊藤幸成、藤田清貴、伏信進矢
    • Organizer
      2017年度生命化学系合同年次大会(ConBio2017)
    • Related Report
      2017 Annual Research Report
  • [Presentation] ビフィズス菌が腸内の糖質を分解するための酵素のかたちと動き2016

    • Author(s)
      伏信進矢
    • Organizer
      日本応用糖質科学会
    • Place of Presentation
      広島県民文化センターふくやま(広島県 福山市)
    • Year and Date
      2016-09-14
    • Related Report
      2016 Research-status Report
    • Invited
  • [Presentation] βーアラビノオリゴ糖鎖に作用するβ-L-アラビノフラノシダーゼの機能解析2015

    • Author(s)
      藤田清貴、亀山恭平、下川倫子、伏信進矢、石渡明弘、Sophon Kaeothip、伊藤幸成、北原兼文
    • Organizer
      第34回日本糖質学会年会
    • Place of Presentation
      東京
    • Year and Date
      2015-07-31
    • Related Report
      2015 Research-status Report
  • [Presentation] チオグリコシド中間体を経由するGH127β-L-アラビノフラノシダーゼの触媒メカニズム2014

    • Author(s)
      伏信進矢
    • Organizer
      第33回日本糖質学会年会
    • Place of Presentation
      名古屋
    • Year and Date
      2014-08-11
    • Related Report
      2014 Research-status Report
    • Invited
  • [Presentation] ビフィズス菌由来 GH127 β-L-アラビノフラノシダーゼの 新規な活性中心2014

    • Author(s)
      伏信進矢
    • Organizer
      第28回セルラーゼ研究会
    • Place of Presentation
      千葉
    • Year and Date
      2014-07-11
    • Related Report
      2014 Research-status Report
    • Invited
  • [Remarks] 東京大学大学院農学生命科学研究科応用生命工学専攻酵素学研究室

    • URL

      http://enzyme13.bt.a.u-tokyo.ac.jp/index.html

    • Related Report
      2014 Research-status Report

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Published: 2014-04-04   Modified: 2019-03-29  

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