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Structural biology for elucidation of lysine biosynthesis and its regulatory mechanisms

Research Project

Project/Area Number 21380057
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Applied microbiology
Research InstitutionThe University of Tokyo

Principal Investigator

NISHIYAMA Makoto  東京大学, 生物生産工学研究センター, 教授 (00208240)

Co-Investigator(Kenkyū-buntansha) TOMITA Takeo  東京大学, 生物生産工学研究センター, 助教 (50447364)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥19,110,000 (Direct Cost: ¥14,700,000、Indirect Cost: ¥4,410,000)
Fiscal Year 2011: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2010: ¥4,550,000 (Direct Cost: ¥3,500,000、Indirect Cost: ¥1,050,000)
Fiscal Year 2009: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000)
Keywords微生物酵素 / 構造生物学 / リジン生合成 / ロイシン生合成 / 超好熱性古細菌 / アルギニン生合成 / 機能分化 / キャリアタンパク質 / X線結晶構造解析 / フィードバック阻害 / ホモクエン酸合成酵素 / アスパラギン酸キナーゼ
Research Abstract

There are two different pathways in lysine biosynthesis. In this study, we have succeeded in elucidation of regulatory mechanisms of enzymes, each of which has a key role in each biosynthetic pathway. In the second half of lysine biosynthetic pathway throughα-aminoadipate, we discovered that a protein named LysW is not only used for modification of the amino group of the substrate, but also served as a carrier protein for biosynthetic enzymes.

Report

(4 results)
  • 2011 Annual Research Report   Final Research Report ( PDF )
  • 2010 Annual Research Report
  • 2009 Annual Research Report
  • Research Products

    (56 results)

All 2012 2011 2010 2009 Other

All Journal Article (19 results) (of which Peer Reviewed: 19 results) Presentation (34 results) Book (1 results) Remarks (2 results)

  • [Journal Article] Evolution of lysine biosynthesis in the phylum Deinococcus-Thermus2012

    • Author(s)
      H.Nishida, M.Nishiyama
    • Journal Title

      International Journal of Evolutionary Biology

      Volume: (In press)

    • Related Report
      2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase2011

    • Author(s)
      T. Tomita, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      J Biol Chem

      Volume: 286 Pages: 37841-37848

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Convergent strategies in biosynthesis2011

    • Author(s)
      T. Dairi, T. Kuzuyama, M. Nishiyama, and I. Fujii
    • Journal Title

      Nat Prod Rep

      Volume: 28 Pages: 1054-1086

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Hetero-oligomeric glutamate dehydrogenase from Thermus thermophilus2010

    • Author(s)
      T. Tomita, T. Miyazaki. J. Miyazaki, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      Microbiology

      Volume: 156 Pages: 3801-3813

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of concerted inhibition ofα_2β_2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum2010

    • Author(s)
      A. Yoshida, T. Tomita, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      J Biol Chem

      Volume: 285 Pages: 27477-27486

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Enhancement of latent 3-isopropylmalate dehydrogenase activity of promiscuous homoisocitrate dehydrogenase by directed evolution2010

    • Author(s)
      Y. Suzuki, K. Asada, J. Miyazaki, T. Tomita, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      Biochem J

      Volume: 431 Pages: 401-410

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus2010

    • Author(s)
      T. Okada, T. Tomita, A. P. Wulandari, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      J Biol Chem

      Volume: 285 Pages: 4195-4205

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Enhancement of latent 3-isopropylmalate dehydrogenase of promiscuous homoisocitrate dehydrogenase by directed evolution2010

    • Author(s)
      Y.Suzuki, ら
    • Journal Title

      Biochemical Journal

      Volume: 431 Pages: 401-410

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of concerted inhibition of α_2β_2-type heterooligomeric aspartate kinase from Corynebacterium glutamicum2010

    • Author(s)
      A.Yoshida, ら
    • Journal Title

      Journal Biological Chemistry

      Volume: 285 Pages: 27477-27486

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Enhancement of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus2010

    • Author(s)
      T.Okada, ら
    • Journal Title

      Journal Biological Chemistry

      Volume: 285 Pages: 4195-4205

    • Related Report
      2010 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discovery of proteinaceous N-modification in lysine biosynthesis of Thermus thermophilus2009

    • Author(s)
      A. Horie, T. Tomita, A. Saiki, H. Kono, H. Taka, R. Mineki, T. Fujimura, C. Nishiyama, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      Nat Chem Biol

      Volume: 5 Pages: 673-679

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Dual roles of a conserved pair, Arg23 and Ser20, in recognition of multiple substrates inα-aminoadipate aminotransferase from Thermus thermophilus2009

    • Author(s)
      T. Ouchi, T. Tomita, T. Miyagawa, Kuzuyama, and M. Nishiyama
    • Journal Title

      Biochem Biophys Res Commun

      Volume: 388 Pages: 2127-2127

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus2009

    • Author(s)
      A. Yoshida, T. Tomita, H. Kono, S. Fushinobu, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      FEBS J

      Volume: 276 Pages: 3124-3136

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism for multiple-substrates recognition ofα-aminoadipate aminotransferase from Thermus thermophilus2009

    • Author(s)
      T. Tomita, T. Miyagawa, T. Miyazaki, S. Fushinobu, T. Kuzuyama, and M. Nishiyama
    • Journal Title

      Proteins

      Volume: 75 Pages: 348-359

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism for multiple-substrates recognition of α-aminoadipate aminotransferase from Thermus thermophilus2009

    • Author(s)
      Tomita, T., et al.
    • Journal Title

      Proteins-Structure Function and Bioinformatics 75

      Pages: 348-359

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structures of the regulatory subunit of Thr-sensitive aspartate kinase from Thermus thermophilus2009

    • Author(s)
      Yoshida, A., et al.
    • Journal Title

      FEBS Journal 276

      Pages: 3124-3136

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Discovery of proleinaceous N-modification in lysine biosynthesis of Thermus thermophilus2009

    • Author(s)
      Horie A., et al.
    • Journal Title

      Nature Chemical Biology 5

      Pages: 673-679

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Dual roles of a conserved pair, Arg23 and Ser20, in recognition of multiple substrates in α-aminoadipate aminotransferase from Thermus thermophilus2009

    • Author(s)
      Ouchi, T., et al.
    • Journal Title

      Biochemical and Biophysical Research Communications 388

      Pages: 21-27

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mechanism of substrate recognition and insight into feedback inhibition of homocitrate synthase from Thermus thermophilus2009

    • Author(s)
      Okada T., et al.
    • Journal Title

      Journal of Biological Chemistry 285

      Pages: 4195-4205

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] リジン・アルギニン生合成機構と進化の解明に向けて2012

    • Author(s)
      西山真
    • Organizer
      日本農芸化学会2012年度大会シンポジウム
    • Place of Presentation
      京都市、京都
    • Year and Date
      2012-03-25
    • Related Report
      2011 Final Research Report
  • [Presentation] リジン・アルギニン生合成機構と進化の解明に向けて2012

    • Author(s)
      西山真
    • Organizer
      日本農芸化学会2012年度大会
    • Place of Presentation
      京都女子大学(招待講演)
    • Year and Date
      2012-03-25
    • Related Report
      2011 Annual Research Report
  • [Presentation] Thermococcus kodakarensisにおけるリジン・アルギニン生合成経路の解析2012

    • Author(s)
      吉田彩子、西山真
    • Organizer
      日本農芸化学会2012年度大会
    • Place of Presentation
      京都市、京都
    • Year and Date
      2012-03-23
    • Related Report
      2011 Final Research Report
  • [Presentation] Analysis of substrate specificity of homoisocitrate dehydrogenase homolog from Thermococcus kodakarensis2012

    • Author(s)
      Yin Lulu、西山真
    • Organizer
      日本農芸化学会2012年度大会
    • Place of Presentation
      京都市、京都
    • Year and Date
      2012-03-23
    • Related Report
      2011 Final Research Report
  • [Presentation] Thermococcus kodakarensisにおけるリジン・アルギニン生合成経路の解析2012

    • Author(s)
      吉田彩子, ら
    • Organizer
      日本農芸化学会2012年度大会
    • Place of Presentation
      京都女子大学
    • Year and Date
      2012-03-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] Analysis of substrate specificity of homoisocitrate dehydrogenase homolog from Thermococcus kodakarensis2012

    • Author(s)
      Lulu Yin, ら
    • Organizer
      日本農芸化学会2012年度大会
    • Place of Presentation
      京都女子大学
    • Year and Date
      2012-03-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] アミノ酸生合成系のパッチワーク仮説2011

    • Author(s)
      西山真
    • Organizer
      理研シンポジウム:生命システム原材料の起源と進化
    • Place of Presentation
      東京
    • Year and Date
      2011-11-26
    • Related Report
      2011 Final Research Report
  • [Presentation] リジン・アルギニン生合成系の共通起源と進化2011

    • Author(s)
      西山真
    • Organizer
      第84会日本生化学会大会シンポジウム
    • Place of Presentation
      京都市、京都
    • Year and Date
      2011-09-21
    • Related Report
      2011 Final Research Report
  • [Presentation] リジン・アルギニン生合成系の共通起源と進化2011

    • Author(s)
      西山真
    • Organizer
      日本生化学会2012年度大会
    • Place of Presentation
      京都国際会議場(招待講演)
    • Year and Date
      2011-09-21
    • Related Report
      2011 Annual Research Report
  • [Presentation] Structural basis for leucine-induced allosteric activation of glutamate dehydrogenase2011

    • Author(s)
      西山真
    • Organizer
      16th Japanese-German Workshop on enzyme Technology
    • Place of Presentation
      富山、富山
    • Year and Date
      2011-09-14
    • Related Report
      2011 Final Research Report
  • [Presentation] Directed evolution of homoisocitrate dehydrogenase to 3-isopropylmalate dehydrogenase2011

    • Author(s)
      西山真
    • Organizer
      IUMS2011 Congress
    • Place of Presentation
      札幌、北海道
    • Year and Date
      2011-09-07
    • Related Report
      2011 Final Research Report
  • [Presentation] リジン/アルギニン生合成系の共通祖先および進化の解明に向けて2011

    • Author(s)
      西山真
    • Organizer
      日本農芸化学会2011年度大会シンポジウム
    • Place of Presentation
      京都女子大学、京都
    • Year and Date
      2011-03-28
    • Related Report
      2011 Final Research Report
  • [Presentation] アミノ酸生合成におけるタンパク質によるアミノ基修飾の普遍性2010

    • Author(s)
      西山真
    • Organizer
      東京大学生物生産工学研究センターシンポジウム
    • Place of Presentation
      文京区、東京
    • Year and Date
      2010-12-08
    • Related Report
      2011 Final Research Report
  • [Presentation] アミノ酸生合成・代謝の調節機構:構造生物学的な視点から2010

    • Author(s)
      西山真
    • Organizer
      東北大学サテライトシンポジウム
    • Place of Presentation
      仙台、宮城
    • Year and Date
      2010-11-26
    • Related Report
      2011 Final Research Report
  • [Presentation] アミノ酸生合成酵素の構造・機能・活性制御に関する基礎・応用研究2010

    • Author(s)
      西山真
    • Organizer
      第11回酵素応用シンポジウム
    • Place of Presentation
      名古屋、愛知
    • Year and Date
      2010-06-11
    • Related Report
      2011 Final Research Report
  • [Presentation] グルタミン酸脱水素酵素の新規活性調節機構の発見2010

    • Author(s)
      西山真、富田武郎
    • Organizer
      日本農芸化学会2010年度大会シンポジウム
    • Place of Presentation
      駒場、東京
    • Year and Date
      2010-03-30
    • Related Report
      2011 Final Research Report
  • [Presentation] グルタミン酸脱水素酵素の新規活性調節機構の発見2010

    • Author(s)
      西山真、富田武郎
    • Organizer
      日本農芸化学会2010年度大会シンポジウム「酵素・タンパク質のユニークな活性調節機構および機能発現の新展開」
    • Place of Presentation
      東京大学
    • Year and Date
      2010-03-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] Thermus thermophilusのリジン生合成酵素LysZおよびキャリアタンパク質の構造機能解析2010

    • Author(s)
      吉田彩子、西山真
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      駒場、東京
    • Year and Date
      2010-03-28
    • Related Report
      2011 Final Research Report
  • [Presentation] 高度好熱菌Thermus thermophilus由来ホモクエン酸合成酵素の活性調節機構の解析2010

    • Author(s)
      岡田卓也、西山真
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      東京、駒場
    • Year and Date
      2010-03-28
    • Related Report
      2011 Final Research Report
  • [Presentation] IPMDH活性を示すよう分子進化させた改変HICDHの構造と機能2010

    • Author(s)
      鈴木夢生、西山真
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      駒場、東京
    • Year and Date
      2010-03-28
    • Related Report
      2011 Final Research Report
  • [Presentation] Thermus thermophilusのリジン生合成酵素LysZおよびキャリアタンパク質LysWの構造機能解析2010

    • Author(s)
      吉田彩子, ら
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      東京大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilus由来ホモクエン酸合成酵素の活性調節機構の解析2010

    • Author(s)
      岡田卓也, ら
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      東京大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] IPMDH活性を示すよう分子進化させた改変HICDHの構造と機能2010

    • Author(s)
      鈴木夢生, ら
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      東京大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilusのグルタミン酸脱水素酵素(GDH)の活性調節サブユニットGdhAの結晶構造解析2010

    • Author(s)
      富田武郎, ら
    • Organizer
      日本農芸化学会2010年度大会
    • Place of Presentation
      東京大学
    • Year and Date
      2010-03-27
    • Related Report
      2009 Annual Research Report
  • [Presentation] リジン生合成の調節機構2010

    • Author(s)
      西山真
    • Organizer
      千葉大学COEスタートアッププログラムシンポジウム「代謝変換プログラムの生体制御への応用」
    • Place of Presentation
      千葉大学
    • Year and Date
      2010-03-10
    • Related Report
      2009 Annual Research Report
  • [Presentation] Carrier protein-mediated lysine/arginine biosynthesis in thermophile2010

    • Author(s)
      西山真
    • Organizer
      Japanese-Swiss Meeting on Biotechnology & Bioprocess Development
    • Place of Presentation
      富山市、富山
    • Related Report
      2011 Final Research Report
  • [Presentation] 旧くて新しいアミノ酸生合成研究2009

    • Author(s)
      西山真
    • Organizer
      富山県立大学生物工学研究センター講演会
    • Place of Presentation
      富山県立大学、富山
    • Year and Date
      2009-12-22
    • Related Report
      2011 Final Research Report
  • [Presentation] 旧くて新しいアミノ酸生合成研究2009

    • Author(s)
      西山真
    • Organizer
      富山県立大学生物工学研究センター講演会
    • Place of Presentation
      富山県立大学
    • Year and Date
      2009-12-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Carrier protein-mediated amino acid biosynthesis2009

    • Author(s)
      Nishiyama, M.
    • Organizer
      15^<th> German-Japanese Workshop on Enzyme Technology
    • Place of Presentation
      ドイツ・ロストック大学
    • Year and Date
      2009-09-26
    • Related Report
      2009 Annual Research Report
  • [Presentation] 好熱菌のユニークなリジン生合成と酵素の構造および機能2009

    • Author(s)
      西山真
    • Organizer
      「微生物の"生体と生態"研究の最前線」シンポジウム
    • Place of Presentation
      筑波大学、筑波
    • Year and Date
      2009-09-14
    • Related Report
      2011 Final Research Report
  • [Presentation] 好熱菌のユニークなリジン生合成系と酵素の構造および機能2009

    • Author(s)
      西山真
    • Organizer
      筑波大学プレ戦略イニシアティブシンポジウム「微生物の"生体と生態"研究の最前線」
    • Place of Presentation
      筑波大学
    • Year and Date
      2009-09-14
    • Related Report
      2009 Annual Research Report
  • [Presentation] 高度好熱菌Thermus thermophilus由来グルタミン酸脱水素酵素における活性調節の分子機構の解析2009

    • Author(s)
      富田武郎, ら
    • Organizer
      理研シンポジウム(高度好熱菌丸ごと-匹プロジェクト 第8回連携研究会)
    • Place of Presentation
      理研播磨研
    • Year and Date
      2009-08-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Thermus thermophilus由来α-アミノアジピン酸アミノ基転移酵素(AAA-AT)の基質認識機構の解析2009

    • Author(s)
      大内拓也, ら
    • Organizer
      理研シンポジウム(高度好熱菌丸ごと-匹プロジェクト 第8回連携研究会)
    • Place of Presentation
      理研播磨研
    • Year and Date
      2009-08-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Carrier-protein mediated amino acid biosynthesis

    • Author(s)
      西山真
    • Organizer
      15th German-Japanese Workshop on Enzyme Technology
    • Place of Presentation
      Rostoc, Germany
    • Related Report
      2011 Final Research Report
  • [Book] バイオサイエンスとインダストリー「リジン生合成の新機構:タンパク質によるアミノ基修飾」2010

    • Author(s)
      西山真
    • Total Pages
      79
    • Publisher
      (財)バイオインダストリー協会
    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://park.itc.u-tokyo.ac.jp/biotec-res-ctr/saiboukinou/

    • Related Report
      2011 Final Research Report
  • [Remarks]

    • URL

      http://park.itc.u-tokyo.ac.ip/biotec-res-ctr/saiboukinou/

    • Related Report
      2009 Annual Research Report

URL: 

Published: 2009-04-01   Modified: 2016-04-21  

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