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

• Project/Area Number: 23770122
• Research Category: Grant-in-Aid for Young Scientists (B)
• Allocation Type: Multi-year Fund
• Research Field: Structural biochemistry
• Research Institution: Kagawa 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: ¥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)
• Keywords: X 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.

Research Products

• [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 site (2013)
  • 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
  • Peer Reviewed
• [Journal Article] Overexpression, crystallization and preliminary X-ray diffraction analysis of L-ribose isomerase from Acinetobacter sp. strain DL-28 (2011)
  • 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
  • Peer Reviewed
• [Journal Article] Crystal structures of rare disaccharides, α-D-glucopyranosyl β-D-psicofuranoside, and α-D-galactopyranosyl β-D-psicofuranoside (2011)
  • 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
  • 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
• [Presentation] X-ray structure of L-ribose isomerase in complex with L-ribose and a deduced catalytic mechanism (2012)
  • 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
• [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
• [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）
• [Presentation] Structure analysis of mutant L-rhamnose isomerase from Pseudomonas stutzeri to elucidate the ring opening mechanism (2011)
  • 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
• [Presentation] X-ray structures of the enzymes used for rare sugar production and their catalytic reaction mechanisms (2011)
  • 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
• [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: Torino, Italy
  • Year and Date: 2011-06-05
• [Presentation] Structure analysis of mutant L-rhamnose isomerase from Pseudomonas stutzeri to elucidate the ring opening mechanism (2011)
  • 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）
• [Presentation] X-ray structures of the enzymes used for rare sugar production and their catalytic reaction mechanisms (2011)
  • 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）
• [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）
• [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）
• [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）
• [Remarks]
  • URL: http://www.med.kagawa-u.ac.jp/~xraylab/
• [Remarks] 科研費報告書
  • URL: http://www.med.kagawa-u.ac.jp/~xraylab/report/kaken/
• [Remarks]
  • URL: http://www.med.kagawa-u.ac.jp/~xraylab/report/kaken/