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Functional analysis of food proteins and food-related enzymes.

Research Project

Project/Area Number 16H04909
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied biochemistry
Research InstitutionKyoto University

Principal Investigator

Mikami Bunzo  京都大学, 農学研究科, 教授 (40135611)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥17,160,000 (Direct Cost: ¥13,200,000、Indirect Cost: ¥3,960,000)
Fiscal Year 2018: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2017: ¥3,770,000 (Direct Cost: ¥2,900,000、Indirect Cost: ¥870,000)
Fiscal Year 2016: ¥9,620,000 (Direct Cost: ¥7,400,000、Indirect Cost: ¥2,220,000)
Keywords構造生物学 / タンパク質工学 / 酵素工学 / X線結晶構造解析 / アミラーゼ / プルラナーゼ / プロテイングルタミナーゼ / 糖質関連酵素 / 食糧関連酵素・タンパク質 / トランスグルタミナーゼ / 糖転移酵素 / x線結晶構造解析 / 食糧関連酵素の構造生物学 / 食糧関連酵素のタンパク質工学 / 食糧関連酵素のX線結晶構造解析 / タンパク質結晶構造解析
Outline of Final Research Achievements

Proteins and enzymes can work through their conformational changes during interaction with substrate and ligands. These conformational changes can be detected by X-ray crystal analysis. But sometimes it is difficult to study about the conformational change owing to bad packing in the crystal lattice. It is also affected by “freezing of protein crystals” and cryo-protectants that usually interact with protein active site. We have to use non-freezing structure especially to observe the effect of pH. In the present work, I have studied about the function of food-related enzymes such as beta-amylase, pullulanase and protein glutaminase by X-ray crystal analysis with freezing and non-freezing (capillary) methods. I could get the fine structure changes in the active site of beta-amylase/substrate complexes caused by pH. The functions of pullulanase and protein glutaminase were also studied using mutant and complex crystals.

Academic Significance and Societal Importance of the Research Achievements

今までに数多くのタンパク質や酵素の構造がX線結晶構造解析によって決定されているが、その働きを理解するためには、実際にタンパク質や酵素が働くところ、つまりタンパク質の構造変化を正しく捕らえる必要がある。本研究では、凍結法のみならず非凍結状態での構造解析を行うことによって食品加工に関連する酵素(β-アミラーゼ、プルラナーゼおよびプロテイングルタミナーゼ)の今まで知られていなかった機能を明らかにすることができた。酵素の働きを正しく理解することによって、より優れた酵素の設計が可能になる。

Report

(4 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Annual Research Report
  • 2016 Annual Research Report
  • Research Products

    (24 results)

All 2019 2018 2017 2016 Other

All Int'l Joint Research (2 results) Journal Article (11 results) (of which Int'l Joint Research: 4 results,  Peer Reviewed: 11 results,  Open Access: 4 results,  Acknowledgement Compliant: 1 results) Presentation (10 results) (of which Int'l Joint Research: 2 results,  Invited: 1 results) Remarks (1 results)

  • [Int'l Joint Research] China Agricultural University(中国)

    • Related Report
      2018 Annual Research Report
  • [Int'l Joint Research] Seoul University(韓国)

    • Related Report
      2018 Annual Research Report
  • [Journal Article] Structure of a serine-type glutathione S-transferase of Ceriporiopsis subvermispora and identification of the enzymatically important non-canonical residues by functional mutagenesis2019

    • Author(s)
      Wan Osman Wan Hasnidah、Mikami Bunzo、Saka Naoki、Kondo Keiko、Nagata Takashi、Katahira Masato
    • Journal Title

      Biochemical and Biophysical Research Communications

      Volume: 510 Issue: 1 Pages: 177-183

    • DOI

      10.1016/j.bbrc.2019.01.076

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] The microenvironment surrounding FAD mediates its conversion to 8-formyl-FAD in Aspergillus oryzae RIB40 formate oxidase.2019

    • Author(s)
      Doubayashi D, Oki M, Mikami B, Uchida H.
    • Journal Title

      J Biochem.

      Volume: 印刷中 Issue: 1 Pages: 67-75

    • DOI

      10.1093/jb/mvz009

    • NAID

      40021952190

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Identification of key residues for activities of atypical glutathione S-transferase of Ceriporiopsis subvermispora, a selective degrader of lignin in woody biomass, by crystallography and functional mutagenesis2019

    • Author(s)
      Osman Wan Hasnidah Wan、Mikami Bunzo、Saka Naoki、Kondo Keiko、Lin Meng-I、Nagata Takashi、Katahira Masato
    • Journal Title

      International Journal of Biological Macromolecules

      Volume: 132 Pages: 222-229

    • DOI

      10.1016/j.ijbiomac.2019.03.199

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] High-resolution crystal structures of the glycoside hydrolase family 45 endoglucanase EG27II from the snail Ampullaria crossean.2019

    • Author(s)
      Nomura T, Iwase H, Saka N, Takahashi N, Mikami B, Mizutani K.
    • Journal Title

      Acta Crystallogr D Struct Biol.

      Volume: 75 Issue: 4 Pages: 426-436

    • DOI

      10.1107/s2059798319003000

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Elucidation of the mechanism of interaction between Klebsiella pneumoniae pullulanase and cyclodextrin.2018

    • Author(s)
      Saka N, Iwamoto H, Malle D, Takahashi N, Mizutani K, Mikami B
    • Journal Title

      Acta Crystallogr D Struct Biol.

      Volume: 74 Issue: 11 Pages: 1115-1123

    • DOI

      10.1107/s2059798318014523

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Structural and thermodynamic characterization of endo-1,3-β-glucanase: Insights into the substrate recognition mechanism2018

    • Author(s)
      M. Oda, S. Inaba, N. Kamiya, G.-J. Bekker, B. Mikami
    • Journal Title

      Biochim. Biophys. Acta, Proteins Proteomics

      Volume: 1866 Issue: 3 Pages: 415-425

    • DOI

      10.1016/j.bbapap.2017.12.004

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of an aldehyde oxidase from Methylobacillus sp. KY44002018

    • Author(s)
      Uchida H., Mikami B., Yamane-Tanabe A., Ito A., Hirano K., Oki M.
    • Journal Title

      J. Biochem.

      Volume: 163 Issue: 4 Pages: 321-328

    • DOI

      10.1093/jb/mvy004

    • NAID

      40021524060

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Alternative substrate-bound conformation of bacterial solute-binding protein involved in the import of mammalian host glycosaminoglycans2017

    • Author(s)
      Oiki Sayoko、Kamochi Reiko、Mikami Bunzo、Murata Kousaku、Hashimoto Wataru
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 17005-17005

    • DOI

      10.1038/s41598-017-16801-8

    • NAID

      120006369452

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Role of the Tyr270 residue in 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase from Mesorhizobium loti.2017

    • Author(s)
      Kobayashi J., Yoshida H., Yagi T., Kamitori S., Hayashi H., Mizutani K., Takahashi N., Mikami B.
    • Journal Title

      J. Biosci. Bioeng.

      Volume: 123 Issue: 2 Pages: 154-162

    • DOI

      10.1016/j.jbiosc.2016.07.022

    • NAID

      40021112404

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Conformational change in the active site of Streptococcal unsaturated glucuronyl hydrolase through site-directed mutagenesis at Asp-1152016

    • Author(s)
      Yusuke Nakamichi, Sayoko Oiki, Bunzo Mikami, Kousaku Murata, and Wataru Hashimoto
    • Journal Title

      The Protein Journal

      Volume: 35 Issue: 4 Pages: 300-309

    • DOI

      10.1007/s10930-016-9673-y

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] "Silent" Amino Acid Residues at Key Subunit Interfaces Regulate the Geometry of Protein Nanocages.2016

    • Author(s)
      Zhang S., Zang J., Zhang X., Chen H., Mikami B., Zhao G.
    • Journal Title

      ACS Nano

      Volume: 10 Issue: 11 Pages: 10382-10388

    • DOI

      10.1021/acsnano.6b06235

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research
  • [Presentation] 結晶構造解析によるアミラーゼの 反応機構の解明2019

    • Author(s)
      三上 文三、坂 直樹、森 湖太郎、水谷 公彦、 高橋 延行
    • Organizer
      日本農芸化学会2019年度大会(東京)
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 細菌の金属輸送に関るEfeUOB系構成アルギン酸結合タンパク質のレアメタル結合性2019

    • Author(s)
      奥村憲史、三上文三、橋本 渉、村田幸作
    • Organizer
      日本農芸化学会2019年度大会(東京)
    • Related Report
      2018 Annual Research Report
  • [Presentation] pH dependent conformational changes of β-amylase/glucose complex crystal measured at room temperature.2018

    • Author(s)
      Bunzo Mikami, Xueni Hou, Kotaro Mori, Motoyasu Adachi, Youna Kang, Kimihiko Mizutani and Nobuyuki Takahashi
    • Organizer
      31st European Crystallographic Meeting
    • Related Report
      2018 Annual Research Report
    • Int'l Joint Research
  • [Presentation] cis-ヒノキレジノール合成酵素による酵素反応の分子機構解明に向けたβサブユニットの X線結晶構造解析2018

    • Author(s)
      東 篤志、坂 直樹、鈴木 史朗、山村 正臣、三上 文三、梅澤 俊明
    • Organizer
      第68回日本木材学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 非凍結結晶を用いたβーアミラーゼ(E380A)と基質との複合体のpH変化の解析2018

    • Author(s)
      三上文三、安達基泰、姜 有那、水谷公彦、高橋延行
    • Organizer
      日本農芸化学会2018年度大会(名古屋)
    • Related Report
      2017 Annual Research Report
  • [Presentation] Klebsiella pneumoniae pullulanase とcyclodextrinとの相互作用様式の解明2018

    • Author(s)
      坂 直樹、田中啓一郎、山野小波、水谷公彦、高橋延行、岩本博行、三上文三
    • Organizer
      日本農芸化学会2018年度大会(名古屋)
    • Related Report
      2017 Annual Research Report
  • [Presentation] X線結晶構造解析と部位特異的変異に基づくプロテイングルタミナーゼの機能解明2018

    • Author(s)
      田中智紀、高橋延行、水谷公彦、山口庄太郎、三上文三
    • Organizer
      日本農芸化学会関西支部例会(第502回講演会)
    • Related Report
      2017 Annual Research Report
  • [Presentation] 非凍結結晶を用いたβ‐アミラーゼ/基質複合体のpHによる構造変化の解析2017

    • Author(s)
      三上文三、河村和広。安達基泰、姜有那、水谷公彦、高橋延行
    • Organizer
      日本農芸化学会
    • Place of Presentation
      京都女子大学
    • Year and Date
      2017-03-18
    • Related Report
      2016 Annual Research Report
  • [Presentation] 貝類由来セルラーゼEG27IIのX線結晶構造解析および機能解析2017

    • Author(s)
      野村泰介、水谷公彦、岩瀬久夢、高橋延行、三上文三
    • Organizer
      日本農芸化学会
    • Place of Presentation
      京都女子大学
    • Year and Date
      2017-03-18
    • Related Report
      2016 Annual Research Report
  • [Presentation] pH Dependent conformational change of bound maltose observed in the crystal of β-amylase at room temperature2016

    • Author(s)
      Bunzo Mikami, Youna Kang, Kimihiko Mizutani, Nobuyuki Takahashi
    • Organizer
      30th Meeting of the European Crystallographic Association
    • Place of Presentation
      Basel, Switzerland
    • Year and Date
      2016-08-28
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research
  • [Remarks] 京都大学農学研究科応用生命科学専攻応用構造生物学分野

    • URL

      http://www.structure.kais.kyoto-u.ac.jp/

    • Related Report
      2018 Annual Research Report 2016 Annual Research Report

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Published: 2016-04-21   Modified: 2020-03-30  

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