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Elucidation of mechanisms for catalytic center maturation and catalysis of nitrile hydratase family enzyme

Research Project

Project/Area Number 21350089
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Chemistry related to living body
Research InstitutionTokyo University of Agriculture and Technology

Principal Investigator

ODAKA Masafumi  東京農工大学, 大学院・工学研究院, 准教授 (20224248)

Co-Investigator(Renkei-kenkyūsha) KUROKI Ryota  独立行政法人日本原子力研究開発機構, 量子ビーム応用研究部門, ユニット長 (30391246)
Project Period (FY) 2009 – 2011
Project Status Completed (Fiscal Year 2011)
Budget Amount *help
¥19,240,000 (Direct Cost: ¥14,800,000、Indirect Cost: ¥4,440,000)
Fiscal Year 2011: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2010: ¥5,720,000 (Direct Cost: ¥4,400,000、Indirect Cost: ¥1,320,000)
Fiscal Year 2009: ¥7,800,000 (Direct Cost: ¥6,000,000、Indirect Cost: ¥1,800,000)
Keywords水和反応 / 加水分解 / 酵素反応 / 結晶構造解析 / 時間分割構造解析 / 翻訳後修飾 / タンパク質成熟化 / アクセサリータンパク質 / 構造生物学 / 中性子 / 生物・生体工学 / バイオリアクター / X線結晶構造解析
Research Abstract

By performing time-resolved X-ray crystallography of Fe-type nitrile hydratase(NHase) whoseβArg56 were substituted by Lys, we obtained the structure of the enzyme-substrate complex. By replacing two Arg residues resided in the active site pocket of a NHase family enzyme, thiocyanate hydrolase(SCNase), we showed that the size as well as the surface charge of the substrate binding pocket was important for the substrate specificities of SCNase. As for the maturation mechanism, we found that the SCNase activator protein, P15K, is responsible for the refolding, metal-insertion and post-translational modification of Cys ligand in the catalytic subunit,γ. The metal-incorporatedγsubunit form the complex with the other subunits,αandβ, to form the mature SCNase.

Report

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

    (51 results)

All 2011 2010 2009 Other

All Journal Article (6 results) (of which Peer Reviewed: 6 results) Presentation (44 results) Remarks (1 results)

  • [Journal Article] Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase2010

    • Author(s)
      Yamanaka Y., Hashimoto K., Ohtaki A., Noguchi K., Yohda M., and Odaka M.
    • Journal Title

      J. Biol. Inorg. Chem

      Volume: 15 Pages: 655-665

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structure and characterization of amidase from Rhodococcus sp. N-771 : Insight into the molecular mechanism of substrate recognition2010

    • Author(s)
      Ohtaki A., Murata K., Sato Y., Noguchi K., Miyatake H., Dohmae N., Yamada K., Yohda M., and Odaka M.
    • Journal Title

      Biochim. Biophys. Acta

      Volume: 1804 Pages: 184-192

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Kinetic and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in nitrile hydratase2010

    • Author(s)
      Yasuaki Yamanaka
    • Journal Title

      Journal of Biological Inorganic chemistry (In press)

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structure and characterization of amidase from Rhodococcus sp. N-771 : Insight into the molecular mechanism of substrate recoenition2010

    • Author(s)
      Akashi Ohtaki
    • Journal Title

      Biochimica Biophysica Acta 1804

      Pages: 184-192

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for catalytic activation of thiocyanate hydrolase involving metal-ligated cysteine modification2009

    • Author(s)
      Arakawa T., Kawano Y., Katayama Y., Nakayama H., Dohmae N., Yohda M., and Odaka M
    • Journal Title

      J. Am. Chem. Soc

      Volume: 131 Pages: 14838-14843

    • Related Report
      2011 Final Research Report
    • Peer Reviewed
  • [Journal Article] Structural basis for catalytic activation of thiocyanate hydrolase involving metal-ligated cysteine modification2009

    • Author(s)
      Takatoshi Arakawa
    • Journal Title

      Journal of American Chemical Society 131

      Pages: 14838-14843

    • Related Report
      2009 Annual Research Report
    • Peer Reviewed
  • [Presentation] Bacillus pallidus RAPc8由来コバルト型ニトリルヒドラターゼの大量発現系構築とキャラクタリゼーション2011

    • Author(s)
      相原敬之、佐藤雅、山中保明、清水敏史、大滝証、野口恵一、養王田正文、尾高雅文
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜市、パシフィコ横浜
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素活性中心近傍アルギニン残基が基質特異性与える影響2011

    • Author(s)
      渡邉俊則、山中保明、荒川孝俊、浪間聡志、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      第34回日本分子生物学会年会
    • Place of Presentation
      横浜市、パシフィコ横浜
    • Year and Date
      2011-12-13
    • Related Report
      2011 Annual Research Report
  • [Presentation] Bacillus pallidus RAPc8由来コバルト型ニトリルヒドラターゼ大量発現系構築とキャラクタリゼーション2011

    • Author(s)
      佐藤雅、山中保明、清水敏史、大滝証、野口恵一、養王田正文、尾高雅文
    • Organizer
      酵素工学研究会第66回講演会
    • Place of Presentation
      文京区本郷・東京大学山上会館
    • Year and Date
      2011-09-29
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の成熟化機構の解明2011

    • Author(s)
      中西拓也、堀祥太、荒川孝俊、浪間聡志、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      酵素工学研究会第66回講演会
    • Place of Presentation
      文京区本郷・東京大学山上会館
    • Year and Date
      2011-09-29
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の成熟化過程の解明2011

    • Author(s)
      中西拓也、堀祥太、荒川孝俊、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      第63回日本生物工学会大会
    • Place of Presentation
      小金井市・東京農工大学
    • Year and Date
      2011-09-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] Bacillus pallidus RAPc8由来コバルト型ニトリルヒドラターゼの大量発現系構築とキャラクタリゼーション2011

    • Author(s)
      佐藤雅、山中保明、清水敏史、大滝証、野口恵一、養王田正文、尾高雅文
    • Organizer
      第63回日本生物工学会大会
    • Place of Presentation
      小金井市・東京農工大学
    • Year and Date
      2011-09-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の基質特異性に対する活性中心近傍アルギニン残基の影響2011

    • Author(s)
      渡邉俊則、荒川孝俊、山中保明、浪間聡志、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      第63回日本生物工学会大会
    • Place of Presentation
      小金井市・東京農工大学
    • Year and Date
      2011-09-27
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の成熟化過程の解明2011

    • Author(s)
      中西拓也、堀祥太、荒川孝俊、浪間聡志、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      第5回バイオ関連化学シンポジウム
    • Place of Presentation
      筑波市・つくば国際会議場「エポカルつくば」
    • Year and Date
      2011-09-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素成熟化における活性化タンパク質の役割~触媒サブユニットとの相互作用解析~2011

    • Author(s)
      渡邉俊則、中西拓也、堀祥太、荒川孝俊、浪間聡志、中山洋、片山葉子、堂前 直、養王田正文、尾高雅文
    • Organizer
      第5回バイオ関連化学シンポジウム
    • Place of Presentation
      筑波市・つくば国際会議場「エポカルつくば」
    • Year and Date
      2011-09-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] Bacillus pallidus RAPc8由来コバルト型ニトリルヒデドラターゼの大量発現系構築とキャラクタリゼーション2011

    • Author(s)
      佐藤雅、山中保明、清水敏史、大滝証、野口恵一、養王田正文、尾高雅文
    • Organizer
      第5回バイオ関連化学シンポジウム
    • Place of Presentation
      筑波市・つくば国際会議場「エポカルつくば」
    • Year and Date
      2011-09-12
    • Related Report
      2011 Annual Research Report
  • [Presentation] Effect of arginine residues around the substrate binding pocket on the substrate specificity of thiocyanate hydrolase2011

    • Author(s)
      YamanakaY., Arakawa T., Namima S., Hori S., Ohtaki A., Noguchi N., Katayama Y., Yohda M., and Odaka M.
    • Organizer
      12th European Biological Inorganic Chemistry Conference
    • Place of Presentation
      Vancouver, Canada
    • Year and Date
      2011-08-10
    • Related Report
      2011 Final Research Report
  • [Presentation] Effect of arginine residues around the substrate binding pocket on the ubstrate specificity of thiocyanate hydrolase2011

    • Author(s)
      Y.Yamanaka, T.Arakawa, S.Namima, S.Hori, A.Ohtaki, K.Noguchi, Y.Katayama, M.Yohda, M.Odaka
    • Organizer
      ICBIC15
    • Place of Presentation
      Vancouver, CANADA
    • Year and Date
      2011-08-10
    • Related Report
      2011 Annual Research Report
  • [Presentation] Catalytic Mechanism of Nitrile Hydratase Proposed by Time-Resolved X-Ray Crystallography2011

    • Author(s)
      Yohda M., Hashimoto K., and Odaka M.
    • Organizer
      The 12th International Conference on QiR(Quality in Resarch)
    • Place of Presentation
      Bali, Indonesia
    • Year and Date
      2011-07-05
    • Related Report
      2011 Annual Research Report 2011 Final Research Report
  • [Presentation] ニトリルヒドラターゼファミリー酵素の基質特異性の解析2011

    • Author(s)
      山中保明、荒川孝俊、浪間聡志、堀祥太、野口恵一、大滝証、片山葉子、養王田正文、尾高雅文
    • Organizer
      第38回生体分子科学討論会
    • Place of Presentation
      筑波市・筑波大学大学会館国際会議室
    • Year and Date
      2011-06-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素基質特異性に対する基質ポケット近傍アルギニン残基の影響2011

    • Author(s)
      山中保明、荒川孝俊、浪間聡志、堀祥太、大滝証、野口恵一、片山葉子、養王田正文、尾高雅文
    • Organizer
      第11回蛋白質科学会年会
    • Place of Presentation
      大阪市・ホテル阪急エキスポパーク
    • Year and Date
      2011-06-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の成熟化過程の解明2011

    • Author(s)
      中西拓也、堀祥太、荒川孝俊、浪間聡志、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      第11回蛋白質科学会年会
    • Place of Presentation
      大阪市・ホテル阪急エキスポパーク
    • Year and Date
      2011-06-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素成熟化における活性化タンパク質の役割~触媒サブユニットとの相互作用解析~2011

    • Author(s)
      渡邉俊則、中西拓也、堀祥太、荒川孝俊、浪間聡志、中山洋、片山葉子、堂前直、養王田正文、尾高雅文
    • Organizer
      第11回蛋白質科学会年会
    • Place of Presentation
      大阪市・ホテル阪急エキスポパーク
    • Year and Date
      2011-06-07
    • Related Report
      2011 Annual Research Report
  • [Presentation] 変異体酵素によるニトリルヒドラターゼファミリー酵素の基質特異性解明2010

    • Author(s)
      山中保明
    • Organizer
      酵素工学研究会第64回講演会
    • Place of Presentation
      東京大学山上会館(東京都)
    • Year and Date
      2010-11-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Rhodococcus erythropolis N771由来-酸化窒素合成酵素遺伝子の発現及び精製2010

    • Author(s)
      前田悠貴
    • Organizer
      酵素工学研究会第64回講演会
    • Place of Presentation
      東京大学山上会館(東京都)
    • Year and Date
      2010-11-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Bacillus pallidus RAP8 由来コバルト型ニトリルヒドラターゼの大量発現系構築とキャラクタリゼーション2010

    • Author(s)
      佐藤雅
    • Organizer
      酵素工学研究会第64回講演会
    • Place of Presentation
      東京大学山上会館(東京都)
    • Year and Date
      2010-11-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Thiobacillus thioparus THI115 由来硫化カルボニル分解酵素COSaseの結晶構造2010

    • Author(s)
      高橋翔平
    • Organizer
      酵素工学研究会第64回講演会
    • Place of Presentation
      東京大学山上会館(東京都)
    • Year and Date
      2010-11-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の成熟化過程におけるコバルト挿入機構2010

    • Author(s)
      中西拓也
    • Organizer
      酵素工学研究会第64回講演会
    • Place of Presentation
      東京大学山上会館(東京都)
    • Year and Date
      2010-11-19
    • Related Report
      2010 Annual Research Report
  • [Presentation] Thiobacillus thioparus THI115 由来硫化カルボニル分解酵素の触媒機構2010

    • Author(s)
      高橋翔平
    • Organizer
      第4回バイオ関連化学シンポジウム
    • Place of Presentation
      大阪大学豊中キャンパス(大阪府)
    • Year and Date
      2010-09-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] ニトリルヒドラターゼにおけるセリン配位子と近傍にある保存されたチロシン残基の機能の構造生物学的解析2010

    • Author(s)
      山中保明
    • Organizer
      第4回バイオ関連化学シンポジウム
    • Place of Presentation
      大阪大学豊中キャンパス(大阪府)
    • Year and Date
      2010-09-25
    • Related Report
      2010 Annual Research Report
  • [Presentation] Biochemical and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in Nitril Hydratase2010

    • Author(s)
      Yamanaka Y., Hashimoto K., Ohtaki A., Noguchi K., Yohda M. and Odaka M.
    • Organizer
      EUROBIC 10(10th European Biological Inorganic Chemistry Conference)
    • Place of Presentation
      Thessaloniki, Greece
    • Year and Date
      2010-07-22
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involving Metal-Ligated Cysteine Modification2010

    • Author(s)
      Odaka M., Arakawa T., Kartayama Y., Nakayama H., Dohmae N., Yohda M.
    • Organizer
      EUROBIC 10(10th European Biological Inorganic Chemistry Conference)
    • Place of Presentation
      Thessaloniki, Greece
    • Year and Date
      2010-07-22
    • Related Report
      2011 Final Research Report
  • [Presentation] Structural Basis for Catalytic Activation of Thiocyanate Hydrolase Involvine Metal-Ligated Cysteine Modification2010

    • Author(s)
      Masafumi Odaka
    • Organizer
      10th European Biological Inorganic Chemistry Conference
    • Place of Presentation
      Aristotle University of Thessaloniki (Thessaloniki)
    • Year and Date
      2010-06-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] Biochemical and structural studies on roles of the serine ligand and a strictly conserved tyrosine residue in Nitril Hydratase2010

    • Author(s)
      Yasuaki Yamanaka
    • Organizer
      10th European Biological Inorganic Chemistry Conference
    • Place of Presentation
      Aristotle University of Thessaloniki (Thessaloniki)
    • Year and Date
      2010-06-22
    • Related Report
      2010 Annual Research Report
  • [Presentation] Bacillus pallidus RAPc8 由来コバルト型ニトリルヒドラターゼの大量発現系構築とキャラクタリゼーション2010

    • Author(s)
      佐藤雅
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] 鉄型ニトリルヒドラタニゼ活性中心におけるセリン配位子と近傍に存在するチロシン残基の機能の構造生物学的解析2010

    • Author(s)
      山中保明
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] チオシアネート加水分解酵素の成熟化過程におけるロバルト挿入機構2010

    • Author(s)
      中西拓也
    • Organizer
      第10回日本蛋白質科学会年会
    • Place of Presentation
      札幌コンベンションセンター(北海道)
    • Year and Date
      2010-06-16
    • Related Report
      2010 Annual Research Report
  • [Presentation] アクリルアミド生産に使われる酵素ニトリルヒドラターゼの反応機構2010

    • Author(s)
      尾高雅文,橋本浩一,山中保明,大滝証,野口恵一,養王田正文
    • Organizer
      日本化学会第90年会ATPシンポジウム「物質・エネルギー変換材料」
    • Place of Presentation
      大阪
    • Year and Date
      2010-03-26
    • Related Report
      2011 Final Research Report
  • [Presentation] アクリルアミド生産に使われる酵素ニトリルヒドラターゼの触媒機構解明の現状2010

    • Author(s)
      尾高雅文
    • Organizer
      H21年度生命物質構造解析研究会
    • Place of Presentation
      東京
    • Year and Date
      2010-01-15
    • Related Report
      2011 Final Research Report
  • [Presentation] 硫化カルボニル分解酵素COSaseの結晶構造解析2009

    • Author(s)
      大滝証
    • Organizer
      酵素工学研究会第62回講演会
    • Place of Presentation
      東京大学山上会館、東京
    • Year and Date
      2009-11-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] 変異体解析による鉄型ニトリルヒドラターゼ触媒反応機構の解析2009

    • Author(s)
      山中保明
    • Organizer
      酵素工学研究会第62回講演会
    • Place of Presentation
      東京大学山上会館、東京
    • Year and Date
      2009-11-13
    • Related Report
      2009 Annual Research Report
  • [Presentation] Thiobacillus thioparus THI115由来硫化カルボニル分解酵素COSaeの結晶構造2009

    • Author(s)
      野口恵一
    • Organizer
      第82回日本生化学会大会
    • Place of Presentation
      神戸国際会議場、兵庫
    • Year and Date
      2009-10-22
    • Related Report
      2009 Annual Research Report
  • [Presentation] Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crystallography using a novel substrate, tert-butylisonitrile2009

    • Author(s)
      Odaka M., Hashimoto, K., Suzuki, H., Taniguchi, K., Noguchi, T., Yohda, M.
    • Organizer
      The 14th International Conference on Biological Inorganic Chemistry(ICBIC14)
    • Place of Presentation
      Nagoya, Japan
    • Year and Date
      2009-07-30
    • Related Report
      2011 Final Research Report
  • [Presentation] Catalytic mechanism of nitrile hydratase proposed by time-resolved X-ray crvstallography using a novel substrate, tert-butylisonitrile2009

    • Author(s)
      Masafumi Odaka
    • Organizer
      The 14th International Conference on Biological Inorganic Chemistry (ICBIC14)
    • Place of Presentation
      名古屋国際会議場、愛知
    • Year and Date
      2009-07-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] Cloning and characterization of nitric oxide synthase from Rhodococcus erythropolis N7712009

    • Author(s)
      Yuki Maeda
    • Organizer
      The 14th International Conference on Biological Inorganic Chemistry (ICBIC14)
    • Place of Presentation
      名古屋国際会議場、愛知
    • Year and Date
      2009-07-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] Catalytic mechanism of nitrile hydratase : Role of Serine ligand and the conserved tyrosine residue2009

    • Author(s)
      山中保明
    • Organizer
      The 14th International Conference on Biological Inorganic Chemistry (ICBIC14)
    • Place of Presentation
      名古屋国際会議場、愛知
    • Year and Date
      2009-07-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] Effect of amino acid residues around the substrate binding pocket on the substrate specificity of thiocyanate hydrolase2009

    • Author(s)
      Satoshi Namima
    • Organizer
      The 14th International Conference on Biological Inorganic Chemistry (ICBIC 14)
    • Place of Presentation
      名古屋国際会議場、愛知
    • Year and Date
      2009-07-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] How does the activator protein, P14K, function on the maturation of cobalt-type nitrile hydratase?2009

    • Author(s)
      Satoshi Shimizu
    • Organizer
      The 14th International Conference on Biological Inorganic Chemistry (ICBIC14)
    • Place of Presentation
      名古屋国際会議場、愛知
    • Year and Date
      2009-07-30
    • Related Report
      2009 Annual Research Report
  • [Presentation] 鉄型ニトリルヒドラターゼ活性中心におけるセリン配位子と近傍のアミノ酸残基の機能2009

    • Author(s)
      山中保明
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテル、熊本
    • Year and Date
      2009-05-20
    • Related Report
      2009 Annual Research Report
  • [Presentation] X線結晶構造解析に基づくRhodococcus sp.N771由来アミダーゼの基質認識機構2009

    • Author(s)
      大滝証
    • Organizer
      第9回日本蛋白質科学会年会
    • Place of Presentation
      熊本全日空ホテル、熊本
    • Year and Date
      2009-05-20
    • Related Report
      2009 Annual Research Report
  • [Remarks]

    • URL

      http://www.tuat.ac.jp/~yohda/index.html

    • Related Report
      2011 Final Research Report

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

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