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X-ray structure analysis of rare sugar producible enzymes aiming for elucidation of novel isomerization mechanism

Research Project

Project/Area Number 23770122
Research Category

Grant-in-Aid for Young Scientists (B)

Allocation TypeMulti-year Fund
Research Field Structural biochemistry
Research InstitutionKagawa University

Principal Investigator

YOSHIDA Hiromi  香川大学, 総合生命科学研究センター, 准教授 (10313305)

Project Period (FY) 2011 – 2012
Project Status Completed (Fiscal Year 2012)
Budget Amount *help
¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2012: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2011: ¥3,120,000 (Direct Cost: ¥2,400,000、Indirect Cost: ¥720,000)
KeywordsX 線結晶解析 / 単糖異性化酵素 / L-ラムノースイソメラーゼ / D-タガトースエピメラーゼ / D-アラビノースイソメラーゼ / L-リボースイソメラーゼ / 希少糖 / 放射光 / 部位特異的変異 / X線結晶解析 / 糖異性化酵素
Research Abstract

X-ray structure of a novel isomerase, L-ribose isomerase from Acinetobacter sp. (L-RI) was determined. L-RI can catalyze reversible isomerization between L-ribose and L-ribulose, and is a plausible enzyme for rare sugar production. In the structure analysis, L-RI showed the dimer formation. The monomer structure of L-RI is similar to that of D-lyxose isomerase from Escherichia coli O157:H7. L-RI retains a metal ion in the active site with three histidines. Two glutamates are putative catalytic residues.

Report

(3 results)
  • 2012 Annual Research Report   Final Research Report ( PDF )
  • 2011 Research-status Report
  • Research Products

    (18 results)

All 2013 2012 2011 Other

All Journal Article (3 results) (of which Peer Reviewed: 3 results) Presentation (12 results) Remarks (3 results)

  • [Journal Article] Structure of L-rhamnose isomerase in complex with L-rhamnopyranose demonstrates the sugar-ring opening mechanism and the role of a substrate sub-binding site2013

    • Author(s)
      Hiromi Yoshida, Akihide Yoshihara, Misa Teraoka, Satoshi Yamashita, Ken Izumori and Shigehiro Kamitori
    • Journal Title

      FEBS Open Bio

      Volume: 3 Issue: 1 Pages: 35-40

    • DOI

      10.1016/j.fob.2012.11.008

    • Related Report
      2012 Annual Research Report 2012 Final Research Report
    • Peer Reviewed
  • [Journal Article] Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-282011

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Akihide Yoshihara, Ken Izumori and Shigehiro Kamitori
    • Journal Title

      Acta crystallogr

      Volume: F 67(10) Issue: 10 Pages: 1281-1284

    • DOI

      10.1107/s1744309111030351

    • Related Report
      2012 Final Research Report 2011 Research-status Report
    • Peer Reviewed
  • [Journal Article] Crystal structures of rare disaccharides, α-D-glucopyranosyl β-D-psicofuranoside, and α-D-galactopyranosyl β-D-psicofuranoside2011

    • Author(s)
      Shigehiro Kamitori, et al
    • Journal Title

      Carbohydr Res

      Volume: 346 Issue: 9 Pages: 1182-1185

    • DOI

      10.1016/j.carres.2011.04.003

    • Related Report
      2012 Final Research Report
    • Peer Reviewed
  • [Presentation] X 線構造解析による Pseudomonas cichorii D-タガトース 3-エピメラーゼにおける 1-deoxy 3-keto-D-galactitol の認識機構に関する研究2012

    • Author(s)
      吉田裕美,茅原静香,吉原明秀,寺岡美沙,石井知彦,何森健,神鳥成弘
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      福岡
    • Year and Date
      2012-12-15
    • Related Report
      2012 Final Research Report
  • [Presentation] X-ray structure of L-ribose isomerase in complex with L-ribose and a deduced catalytic mechanism2012

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Akihide Yoshihara, Ken Izumori and Shigehiro Kamitori
    • Organizer
      22nd IUBMB 37th FEBS Congress
    • Place of Presentation
      Sevilla, Spain
    • Year and Date
      2012-09-05
    • Related Report
      2012 Final Research Report
  • [Presentation] 糖環開環機構の解明を目指したPseudomonas stutzeri 由来 L-ラムノースイソメラーゼ変異酵素の構造解析2012

    • Author(s)
      吉田裕美,寺岡美沙,何森健, 神鳥成弘
    • Organizer
      2012 年度農芸化学会大会
    • Place of Presentation
      京都
    • Year and Date
      2012-03-25
    • Related Report
      2012 Final Research Report
  • [Presentation] 糖環開環機構の解明を目指したPseudomonas stutzeri 由来 L-ラムノースイソメラーゼ変異酵素の構造解析2012

    • Author(s)
      吉田裕美、寺岡美沙、何森健、神鳥成弘
    • Organizer
      2012年度農芸化学会大会
    • Place of Presentation
      京都女子大(京都)
    • Related Report
      2011 Research-status Report
  • [Presentation] Structure analysis of mutant L-rhamnose isomerase from Pseudomonas stutzeri to elucidate the ring opening mechanism2011

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Ken Izumori and Shigehiro Kamitori
    • Organizer
      Rare Sugar Congress 2011
    • Place of Presentation
      Takamatsu, Japan
    • Year and Date
      2011-11-11
    • Related Report
      2012 Final Research Report
  • [Presentation] X-ray structures of the enzymes used for rare sugar production and their catalytic reaction mechanisms2011

    • Author(s)
      Hiromi Yoshida, Mitsugu Yamada, Kosei Takeda, Takeyori Nishitani, Yuya Ohyama, Masatsugu Yamaji, Tomohiko Ishii, Goro Takada, Ken Izumori and Shigehiro Kamitori
    • Organizer
      Rare Sugar Congress 2011
    • Place of Presentation
      Takamatsu, Japan
    • Year and Date
      2011-11-09
    • Related Report
      2012 Final Research Report
  • [Presentation] Crystal structure of a rare sugar producible enzyme L-ribose isomerase from Acinetobacter sp2011

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Akihide Yoshihara, Ken Izumori and Shigehiro Kamitori
    • Organizer
      36th FEBS Congress
    • Place of Presentation
      Torino, Italy
    • Year and Date
      2011-06-05
    • Related Report
      2012 Final Research Report
  • [Presentation] Structure analysis of mutant L-rhamnose isomerase from Pseudomonas stutzeri to elucidate the ring opening mechanism2011

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Ken Izumori and Shigehiro Kamitori
    • Organizer
      Rare Sugar Congress 2011
    • Place of Presentation
      香川大学農学部(香川)
    • Related Report
      2011 Research-status Report
  • [Presentation] X-ray structures of the enzymes used for rare sugar production and their catalytic reaction mechanisms2011

    • Author(s)
      Hiromi Yoshida, Mitsugu Yamada, Kosei Takeda, Takeyori Nishitani, Yuya Ohyama, Masatsugu Yamaji, Tomohiko Ishii, Goro Takada, Ken Izumori and Shigehiro Kamitori
    • Organizer
      Rare Sugar Congress 2011
    • Place of Presentation
      かがわ国際会議場(香川)
    • Related Report
      2011 Research-status Report
  • [Presentation] Crystal structure of a rare sugar producible enzyme L-ribose isomerase from Acinetobacter sp.2011

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Akihide Yoshihara, Ken Izumori and Shigehiro Kamitori
    • Organizer
      36th FEBS Congress
    • Place of Presentation
      Lingotto Conference Centre(イタリア)
    • Related Report
      2011 Research-status Report
  • [Presentation] X線構造解析によるPseudomonas cichorii D-タガトース 3-エピメラーゼにおける1-deoxy 3-keto-D-galactitol の認識機構に関する研究

    • Author(s)
      吉田裕美, 茅原静香, 吉原明秀, 寺岡美沙, 石井知彦, 何森健, 神鳥成弘
    • Organizer
      第85回日本生化学会大会
    • Place of Presentation
      マリンメッセ福岡(福岡)
    • Related Report
      2012 Annual Research Report
  • [Presentation] X-ray structure of L-ribose isomerase in complex with L-ribose and a deduced catalytic mechanism

    • Author(s)
      Hiromi Yoshida, Misa Teraoka, Akihide Yoshihara, Ken Izumori and Shigehiro Kamitori
    • Organizer
      22nd IUBMB 37th FEBS Congress
    • Place of Presentation
      Sevilla (スペイン)
    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.med.kagawa-u.ac.jp/~xraylab/

    • Related Report
      2012 Final Research Report
  • [Remarks] 科研費報告書

    • URL

      http://www.med.kagawa-u.ac.jp/~xraylab/report/kaken/

    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://www.med.kagawa-u.ac.jp/~xraylab/report/kaken/

    • Related Report
      2011 Research-status Report

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Published: 2011-08-05   Modified: 2019-07-29  

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