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Repression of growth of pathogens on the basis of iron uptake systems

Research Project

Project/Area Number 16K05835
Research Category

Grant-in-Aid for Scientific Research (C)

Allocation TypeMulti-year Fund
Section一般
Research Field Bio-related chemistry
Research InstitutionHokkaido University

Principal Investigator

Uchida Takeshi  北海道大学, 理学研究院, 准教授 (30343742)

Project Period (FY) 2016-04-01 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥5,070,000 (Direct Cost: ¥3,900,000、Indirect Cost: ¥1,170,000)
Fiscal Year 2018: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000)
Fiscal Year 2017: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Fiscal Year 2016: ¥1,820,000 (Direct Cost: ¥1,400,000、Indirect Cost: ¥420,000)
Keywordsタンパク質 / ヘムタンパク質 / 酵素 / 反応機構解析 / 構造解析 / 病原菌 / ヘム / 鉄 / 反応機構 / 蛋白質 / 酵素反応 / 細菌 / 生体分子
Outline of Final Research Achievements

Iron is an essential element for bacterial growth because it is contained in proteins playing key roles in metabolic processes. Most irons in the human body are present as a heme iron. Therefore, heme is a dominant iron source for most pathogens. In this project the reaction mechanism of a heme-degrading enzyme HutZ from V. cholerae was solved. We found that iron chelators are able to inhibit HutZ by perturbing the proton transfer to heme intermediate. This mechanism suggests that iron chelators are candidates of antibiotics. We further found that heme binds to iron-carrier protein CyaY and PBGD that catalyzes the polymerization of porphobilinogen to form 1-hydroxymethylbilane. Heme binding to CyaY and PBGD resulted in less activity, indicating the presence of heme-induced negative feedback. These were not observed in the corresponding human proteins. Therefore, we can propose that HutZ, CyaY and PBGD are good target for new medicine to repress pathogen growth without side reaction.

Academic Significance and Societal Importance of the Research Achievements

今回の発見の一つであるHutZの活性制御機構は、二量体の界面構造の変化を通じて行っているが、ヒトが保有するヘム分解酵素は単量体のタンパク質であり、コレラ菌由来HutZに特有な性質である。そのため、この界面構造を抑制する分子が存在すれば、コレラ菌の鉄獲得機構をのみを選択的に抑制することが可能である。キレート能をもつ小分子がHutZの反応を抑制するなど候補となる分子も発見した。それ以外にも今回発見した多くの事象はコレラ菌などの病原菌がもつタンパク質に特有な性質である。今後は本研究課題により見出された多くの性質を利用するこでで、従来型とは異なる新規な機構の阻害剤の開発につながることが期待される。

Report

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

    (31 results)

All 2019 2018 2017 2016 Other

All Journal Article (11 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 11 results,  Acknowledgement Compliant: 2 results,  Open Access: 3 results) Presentation (18 results) (of which Int'l Joint Research: 1 results,  Invited: 1 results) Remarks (2 results)

  • [Journal Article] Subunit-subunit interactions play a key role in the heme-degradation reaction of HutZ from Vibrio cholerae2019

    • Author(s)
      Uchida Takeshi、Ota Kazuki、Sekine Yukari、Dojun Nobuhiko、Ishimori Koichiro
    • Journal Title

      Dalton Transactions

      Volume: 48 Issue: 12 Pages: 3973-3983

    • DOI

      10.1039/c9dt00604d

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Role of His63 in HutZ from Vibrio cholerae in the heme degradation reaction and heme binding2019

    • Author(s)
      Uchida*, T., Dojun, N., Sekine, Y., and Ishimori, K.
    • Journal Title

      Dalton Transactions

      Volume: 48 Pages: 5408-5416

    • NAID

      120006841053

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Heme binding to porphobilinogen deaminase from Vibrio cholerae decelerates the formation of 1-hydroxymethylbilane2018

    • Author(s)
      Uchida*, T., Funamizu, T., Chen, M., Tanaka, Y., and Ishimori, K.
    • Journal Title

      ACS Chemical Biology

      Volume: 15 Issue: 3 Pages: 750-760

    • DOI

      10.1021/acschembio.7b00934

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] The Iron Chaperone Protein CyaY from Vibrio cholerae is a Heme-Binding Protein2017

    • Author(s)
      Uchida, T., Kobayashi, N., Muneta, S., Ishimori, K.
    • Journal Title

      Biochemistry

      Volume: 印刷中 Issue: 18 Pages: 2425-2434

    • DOI

      10.1021/acs.biochem.6b01304

    • Related Report
      2017 Research-status Report 2016 Research-status Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Heme iron coordination structure of heme transport protein HutB from Vibrio cholerae2017

    • Author(s)
      Uchida*, T., Funamizu, T., Ogura, M., and Ishimori, K.
    • Journal Title

      Bulletin of the Chemical Society of Japan

      Volume: 90 Issue: 8 Pages: 924-930

    • DOI

      10.1246/bcsj.20170104

    • NAID

      130005973696

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access
  • [Journal Article] Heme proximal hydrogen bonding between His170 and Asp132 plays an essential role in the heme degradation reaction by HutZ from Vibrio cholerae2017

    • Author(s)
      Uchida*, T., Dojun, N., Sekine, Y., and Ishimori, K.
    • Journal Title

      Biochemistry

      Volume: 56 Issue: 21 Pages: 2723-2734

    • DOI

      10.1021/acs.biochem.7b00152

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Reaction Intermediates in the heme degradation reaction by HutZ from Vibrio cholerae2017

    • Author(s)
      Uchida*, T., Sekine, Y., Dojun, N., Lewis, A., Ishigami, I., Matsui, T., Yeh, S.-R., and Ishimori, K.
    • Journal Title

      Dalton Transactions

      Volume: 46 Issue: 25 Pages: 8104-8109

    • DOI

      10.1039/c7dt01562c

    • NAID

      120006486794

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] Iron chelators inhibit the heme-degradation reaction by HutZ from Vibrio cholerae2017

    • Author(s)
      Dojun, N., Sekine, Y., Ishimori, K., Uchida, T.
    • Journal Title

      Dalton Transactions

      Volume: 46 Issue: 16 Pages: 5147-5150

    • DOI

      10.1039/c7dt00121e

    • NAID

      120006459301

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Dual role of the active-center cysteine in human peroxiredoxin 1: Peroxidase activity and heme binding2017

    • Author(s)
      Watanabe, Y., Ishimori, K., Uchida, T.
    • Journal Title

      Biochemical and Biophysical Research Communication

      Volume: 483 Issue: 3 Pages: 930-935

    • DOI

      10.1016/j.bbrc.2017.01.034

    • NAID

      120006383811

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] HmuS from Yersinia pseudotuberculosis is a non-canonical heme-degrading enzyme to acquire iron from heme2017

    • Author(s)
      Onzuka, M., Sekine, Y., Uchida, T., Ishimori, K., and Ozaki, S.
    • Journal Title

      Biochimica et Biophysica Acta

      Volume: 印刷中 Issue: 7 Pages: 1870-1878

    • DOI

      10.1016/j.bbagen.2017.04.003

    • Related Report
      2016 Research-status Report
    • Peer Reviewed
  • [Journal Article] Structural Characterization of Heme Environmental Mutants of CgHmuT that Shuttles Heme Molecules to Heme Transporters2016

    • Author(s)
      N. Muraki, C. Kitatsuji, M. Ogura, T. Uchida, K. Ishimori, and S. Aono
    • Journal Title

      Int. J. Mol. Sci.

      Volume: 17 Issue: 6 Pages: 829-839

    • DOI

      10.3390/ijms17060829

    • Related Report
      2016 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] シアノバクテリア由来Alr5027の1残基変異によるヘム分解能の付与2019

    • Author(s)
      道順 暢彦、石森 浩一郎、内田 毅
    • Organizer
      日本化学会第99春季年会
    • Related Report
      2018 Annual Research Report
  • [Presentation] ヘム合成関連酵素ポルフォビリノーゲンデアミナーゼ (PBGD)のヘム結合による活性制御2018

    • Author(s)
      船水 拓実、石森 浩一郎、内田 毅
    • Organizer
      第45回生体分子科学討論会
    • Related Report
      2018 Annual Research Report
  • [Presentation] DyP型ペルオキシダーゼの色素分解活性の至適pH変換2018

    • Author(s)
      大村 翼世、石森 浩一郎、内田 毅
    • Organizer
      第28回金属の関与する生体関連反応シンポジウム
    • Related Report
      2018 Annual Research Report
  • [Presentation] 過酸化水素除去酵素ペルオキシレドキシンのヘム結合による活性制御2017

    • Author(s)
      渡部 裕太、石森 浩一郎、内田 毅
    • Organizer
      日本化学会第97春季年会
    • Place of Presentation
      慶應義塾大学(神奈川県・横浜市)
    • Year and Date
      2017-03-16
    • Related Report
      2016 Research-status Report
  • [Presentation] ヘムの結合による鉄シャペロンタンパク質CyaYの活性制御2017

    • Author(s)
      小林 則之、宗田 壮一朗、石森 浩一郎、内田 毅
    • Organizer
      第27回金属の関与する生体関連反応シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] コレラ菌由来ヘム分解酵素 HutZ のヘム分解機構の詳細2017

    • Author(s)
      内田 毅、道順 暢彦、関根 由可里、石森 浩一郎
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] 分子進化的手法を用いたコレラ菌由来HutZのヘム分解機能の獲得機構の解明2017

    • Author(s)
      道順 暢彦、関根 由可里、石森 浩一郎、内田 毅
    • Organizer
      第11回バイオ関連化学シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] Heme Uptake Proteins from Pathogenic Vibrio cholerae2017

    • Author(s)
      T. Uchida
    • Organizer
      International Congress on Pure & Applied Chemistry (ICPAC) 2018
    • Related Report
      2017 Research-status Report
    • Int'l Joint Research / Invited
  • [Presentation] ヘム合成酵素PBGDのヘム結合による活性制御2017

    • Author(s)
      船水 拓実、石森 浩一郎、内田 毅
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] コレラ菌由来HutZの二量体界面構造のヘム分解活性への寄与2017

    • Author(s)
      大田 一喜、道順 暢彦、石森 浩一郎、内田 毅
    • Organizer
      日本化学会第98春季年会
    • Related Report
      2017 Research-status Report
  • [Presentation] ヘム合成系酵素porphobilinogen deaminaseのヘムによる制御機構2016

    • Author(s)
      船水 拓実、内田 毅
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県・金沢市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] キレート剤によるコレラ菌由来ヘム分解酵素 HutZ の活性阻害とその分子機構2016

    • Author(s)
      道順 暢彦、関根 由可里、内田 毅
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県・金沢市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] ヘムから鉄の引き抜きと色素分解を行う二刀流タンパク質VcDyPの構造と反応機構2016

    • Author(s)
      佐々木 美穂、石森 浩一郎、内田 毅
    • Organizer
      第10回バイオ関連化学シンポジウム
    • Place of Presentation
      石川県立音楽堂(石川県・金沢市)
    • Year and Date
      2016-09-07
    • Related Report
      2016 Research-status Report
  • [Presentation] キレート剤によるコレラ菌由来ヘム分解酵素HutZの活性阻害とその分子機構2016

    • Author(s)
      道順 暢彦、関根 由可里、石森 浩一郎、内田 毅
    • Organizer
      第4回バイオ関連化学シンポジウム若手フォーラム
    • Place of Presentation
      金沢駅東もてなしドーム地下イベント広場(石川県・金沢市)
    • Year and Date
      2016-09-06
    • Related Report
      2016 Research-status Report
  • [Presentation] コレラ菌由来ヘム分解酵素HutZのヘム分解反応機構2016

    • Author(s)
      関根 由可里、石森 浩一郎、内田 毅
    • Organizer
      第43回生体分子科学討論会
    • Place of Presentation
      名古屋大学野依記念学術交流館(愛知県・岡崎市)
    • Year and Date
      2016-06-24
    • Related Report
      2016 Research-status Report
  • [Presentation] キレート剤によるヘム分解酵素HutZの酵素活性阻害機構2016

    • Author(s)
      道順 暢彦、関根 由可里、石森 浩一郎、内田 毅
    • Organizer
      第26回金属の関与する生体関連反応シンポジウム
    • Place of Presentation
      北海道大学学術交流会館(北海道・札幌市)
    • Year and Date
      2016-06-17
    • Related Report
      2016 Research-status Report
  • [Presentation] ヘム合成に関わる酵素Porphobilinogen deaminaseのヘムによるフィードバック制御2016

    • Author(s)
      船水 拓実、石森 浩一郎、内田 毅
    • Organizer
      第26回金属の関与する生体関連反応シンポジウム
    • Place of Presentation
      北海道大学学術交流会館(北海道・札幌市)
    • Year and Date
      2016-06-17
    • Related Report
      2016 Research-status Report
  • [Presentation] コレラ菌由来HutXによるヘム分解酵素HutZへのヘム輸送2016

    • Author(s)
      関根 由可里、石森 浩一郎、内田 毅
    • Organizer
      第26回金属の関与する生体関連反応シンポジウム
    • Place of Presentation
      北海道大学学術交流会館(北海道・札幌市)
    • Year and Date
      2016-06-17
    • Related Report
      2016 Research-status Report
  • [Remarks] 研究室ニュース

    • URL

      http://wwwchem.sci.hokudai.ac.jp/~stchem/news/1103/

    • Related Report
      2016 Research-status Report
  • [Remarks] 発表論文からpickup

    • URL

      http://wwwchem.sci.hokudai.ac.jp/~stchem/pickup/

    • Related Report
      2016 Research-status Report

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

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