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Structural basis of ATP hydrolysis mechanism of V1-ATPase motor

Research Project

Project/Area Number 23370047
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypeSingle-year Grants
Section一般
Research Field Structural biochemistry
Research InstitutionChiba University

Principal Investigator

MURATA Takeshi  千葉大学, 理学(系)研究科(研究院), 准教授 (80415322)

Co-Investigator(Kenkyū-buntansha) YAMATO Ichiro  東京理科大学, 基礎工学部, 教授 (70111458)
Co-Investigator(Renkei-kenkyūsha) SAIJO Shinya  東京理科大学, 基礎工学部, 助教 (80419001)
MIZUTANI Kenji  東京理科大学, 基礎工学部, 博士研究員 (10525570)
Project Period (FY) 2011-04-01 – 2014-03-31
Project Status Completed (Fiscal Year 2013)
Budget Amount *help
¥14,950,000 (Direct Cost: ¥11,500,000、Indirect Cost: ¥3,450,000)
Fiscal Year 2013: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2012: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
Fiscal Year 2011: ¥10,010,000 (Direct Cost: ¥7,700,000、Indirect Cost: ¥2,310,000)
Keywords分子モーター / 酵素反応 / V-ATPase / X線結晶構造解析 / ATP
Research Abstract

Vacuolar ATPases (V-ATPases) function as proton pumps in various membrane systems within the cells, which are involved in a number of processes such as bone resorption and cancer metastasis. The hydrophilic V1 portion is known as a rotary motor, in which a central axis DF complex rotates inside a hexagonally arranged catalytic A3B3 complex using ATP hydrolysis energy, although the molecular mechanism is not well defined due to a lack of high-resolution structural information.
We have established the in vitro expression, purification, and reconstitution of Enterococcus hirae V1-ATPase from the A3B3 and DF complexes. In this study, we solved the crystal structures of AMP-PNP-bound and Pi-bound V1-ATPase, and also characterized the several site-directed mutants. On the basis of these findings, we proposed the molecular mechanism of the rotary motor.

Report

(4 results)
  • 2013 Annual Research Report   Final Research Report ( PDF )
  • 2012 Annual Research Report
  • 2011 Annual Research Report
  • Research Products

    (42 results)

All 2014 2013 2012 2011 Other

All Journal Article (10 results) (of which Peer Reviewed: 10 results) Presentation (18 results) (of which Invited: 4 results) Book (12 results) Remarks (2 results)

  • [Journal Article] Mutant LV476-7AA of A-subunit of Enterococcus hirae V 1-ATPase : High affinity of A3B3 complex to DF axis and low ATPase activity2013

    • Author(s)
      Md. Jahangir Alam, Ichiro Yamato, Satoshi Arai, Shinya Saijo, Kenji Mizutani, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Yoshimi Kakinuma and Takeshi Murata
    • Journal Title

      SpringerPlus

      Volume: 2 Pages: 689-689

    • Related Report
      2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Basic properties of rotary dynamics of the molecular motor Enterococcus hirae V1-ATPase2013

    • Author(s)
      Yoshihiro Minagawa, Hiroshi Ueno, Mayu Hara, Yoshiko Ishizuka-Katsura, Noboru Ohsawa,Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, Ichiro Yamato, Eiro Muneyuki, Hiroyuki Noji, Takeshi Murata, and Ryota Iino
    • Journal Title

      J.Biol.Chem

      Volume: 288 Issue: 45 Pages: 32700-32707

    • DOI

      10.1074/jbc.m113.506329

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Loose Binding of the DF Axis with the A 3B3 Complex Stimulates the Initial Activity of Enterococcus hirae V 1-ATPase2013

    • Author(s)
      Md. Jahangir Alam, Satoshi Arai, Shinya Saijo, Kano Suzuki, Kenji Mizutani, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Yoshimi Kakinuma, Ichiro Yamato and Takeshi Murata
    • Journal Title

      PLoS ONE

      Volume: 8 Issue: 9 Pages: e74291-e74291

    • DOI

      10.1371/journal.pone.0074291

    • Related Report
      2013 Annual Research Report 2013 Final Research Report
    • Peer Reviewed
  • [Journal Article] Biochemical and biophysical properties of interactions between subunits of the peripheral stalk region of human V-ATPase2013

    • Author(s)
      Suhaila Rahman, Ichiro Yamato, Shinya Saijo, Kenji Mizutani, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata and Takeshi Murata
    • Journal Title

      PLoS ONE

      Volume: 8 Issue: 2 Pages: e55704-e55704

    • DOI

      10.1371/journal.pone.0055704

    • Related Report
      2013 Final Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Rotation mechanism of Enterococcus hirae V 1-ATPase based on asymmetric crystal structures2013

    • Author(s)
      Satoshi Arai, Shinya Saijo, Kano Suzuki, Kenji Mizutani, Yoshimi Kakinuma, Yoshiko Ishizuka-Katsura, Noboru, Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Ichiro Yamato and Takeshi Murata
    • Journal Title

      Nature

      Volume: 493 Issue: 7434 Pages: 703-707

    • DOI

      10.1038/nature11778

    • Related Report
      2013 Final Research Report 2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mutant LV476-7AA of A-subunit of Enterococcus hirae V1-ATPase: High affinity of A3B3 complex to DF axis and low ATPase activity2013

    • Author(s)
      Md. Jahangir Alam, Ichiro Yamato, Satoshi Arai, Shinya Saijo, Kenji Mizutani, Yoshiko Ishizuka-Katsura, Noboru Ohsawa, Takaho Terada, Mikako Shirouzu, Shigeyuki Yokoyama, So Iwata, Yoshimi Kakinuma and Takeshi Murata
    • Journal Title

      SpringerPlus

      Volume: 2 Pages: 689-689

    • Related Report
      2013 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mutagenesis of the residues forming an ion binding pocket of the NtpK subunit of Enterococcus hirae V-ATPase2012

    • Author(s)
      Miyuki Kawano-Kawada
    • Journal Title

      J. Bacteriol.

      Volume: 194 Issue: 17 Pages: 4546-4549

    • DOI

      10.1128/jb.00714-12

    • Related Report
      2012 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Sarkosyl is a good regeneration reagent for studies on vacuolar-type ATPase subunit interactions in Biacore experiments2011

    • Author(s)
      Suhaila Rahman, Satoshi Arai, Shinya Saijo, Ichiro Yamato, and Takeshi Murata
    • Journal Title

      Anali. Biochem

      Volume: 418 Issue: 2 Pages: 301-303

    • DOI

      10.1016/j.ab.2011.07.009

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Mass Spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding2011

    • Author(s)
      Min Zhou, Nina Morgner, Nelson P. Barrera, Argyris Politis, Shoshanna C Isaacson, Dijana Matak-Vinković, Takeshi Murata, Ricardo A. Bernal, Daniela Stock and Carol V. Robinson
    • Journal Title

      Science

      Volume: 334 Issue: 6054 Pages: 380-385

    • DOI

      10.1126/science.1210148

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Crystal structure of the central axis DF complex of the prokaryotic V-ATPase2011

    • Author(s)
      Saijo, S.
    • Journal Title

      Pioc Natl Acad Sci USA

      Volume: 108 Issue: 50 Pages: 19955-19960

    • DOI

      10.1073/pnas.1108810108

    • Related Report
      2013 Final Research Report 2011 Annual Research Report
    • Peer Reviewed
  • [Presentation] Rotation mechanism of V-ATPase based on crystal structures2014

    • Author(s)
      Takeshi Murata
    • Organizer
      Gordon Research Conference (Protons and Membrane Reactions)
    • Place of Presentation
      Ventura( アメリカ)
    • Year and Date
      2014-02-27
    • Related Report
      2013 Final Research Report
  • [Presentation] Rotation mechanism of V-ATPase based on crystal structures2014

    • Author(s)
      Takeshi Murata
    • Organizer
      Gordon Research Conference (Protons and Membrane Reactions)
    • Place of Presentation
      Ventura(アメリカ)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 創薬につながるV-ATPaseの構造と機能2013

    • Author(s)
      村田武士
    • Organizer
      第86回生化学会シンポジウム
    • Place of Presentation
      横浜
    • Year and Date
      2013-09-12
    • Related Report
      2013 Final Research Report
  • [Presentation] Rotation mechanism of V1-ATPase based on asymmetric crystal structures2013

    • Author(s)
      Takeshi Murata
    • Organizer
      International Conference on Structural Genomics 2013
    • Place of Presentation
      Sapporo
    • Year and Date
      2013-07-31
    • Related Report
      2013 Annual Research Report 2013 Final Research Report
  • [Presentation] Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures2013

    • Author(s)
      Takeshi Murata
    • Organizer
      Gordon Research Conference in Molecular and Cellular Bioenergetics
    • Place of Presentation
      New Hampshire (アメリカ)
    • Year and Date
      2013-06-26
    • Related Report
      2013 Final Research Report
  • [Presentation] Rotation mechanism of Enterococcus hirae V1-ATPase based on asymmetric crystal structures2013

    • Author(s)
      Takeshi Murata
    • Organizer
      Gordon Research Conference in Molecular and Cellular Bioenergetics
    • Place of Presentation
      New Hampshire(アメリカ)
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] 創薬につながるV-ATPaseの構造と機能2013

    • Author(s)
      村田 武士
    • Organizer
      第86回生化学会
    • Place of Presentation
      横浜
    • Related Report
      2013 Annual Research Report
    • Invited
  • [Presentation] Crystallization of membrane proteins using functional antibody fragments2012

    • Author(s)
      Takeshi Murata
    • Organizer
      AsCA 12/CRYSTAL 28 and Bragg Centennial Symposium
    • Place of Presentation
      オーストラリア(アデレード)
    • Year and Date
      2012-12-03
    • Related Report
      2013 Final Research Report
  • [Presentation] Crystallization of membrane proteins using functional antibody fragments2012

    • Author(s)
      Takeshi Murata
    • Organizer
      AsCA 12/CRYSTAL 28
    • Place of Presentation
      オーストラリア(アデレード)
    • Related Report
      2012 Annual Research Report
    • Invited
  • [Presentation] V1-ATPase のX線結晶構造解析2011

    • Author(s)
      村田武士
    • Organizer
      第37回生体エネルギー研究会
    • Place of Presentation
      京都
    • Year and Date
      2011-12-22
    • Related Report
      2013 Final Research Report
  • [Presentation] V1-ATPaseのX線結晶構造解析2011

    • Author(s)
      村田武士
    • Organizer
      第37回生体エネルギー研究会
    • Place of Presentation
      京都産業大学(京都府)
    • Year and Date
      2011-12-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] 腸球菌由来ヌクレオチド結合型V_1-ATPaseのX線結晶構造解析2011

    • Author(s)
      鈴木花野
    • Organizer
      第84回生化学会
    • Place of Presentation
      京都国際会館(京都府)
    • Year and Date
      2011-09-23
    • Related Report
      2011 Annual Research Report
  • [Presentation] Enterococcus hirae 由来V1-ATPaseの結晶構造解析2011

    • Author(s)
      西條慎也
    • Organizer
      第84回生化学会
    • Place of Presentation
      京都
    • Year and Date
      2011-09-22
    • Related Report
      2013 Final Research Report
  • [Presentation] Enterococcus hirae由来V_1-ATPaseの結晶構造解析2011

    • Author(s)
      西條慎也
    • Organizer
      第84回生化学会
    • Place of Presentation
      京都国際会館(京都府)
    • Year and Date
      2011-09-22
    • Related Report
      2011 Annual Research Report
  • [Presentation] Crystal structure of V1-ATPase from Enterococcus hirae2011

    • Author(s)
      Takeshi Murata
    • Organizer
      Gordon Research Conference in Molecular and Cellular Bioenergetics
    • Place of Presentation
      New Hampshire (アメリカ)
    • Year and Date
      2011-06-30
    • Related Report
      2013 Final Research Report
  • [Presentation] Crystal structure of V1-ATPase from Enterococcus hirae2011

    • Author(s)
      村田武士
    • Organizer
      Gordon Research Conference in Molecular and Cellular Bioenergetics
    • Place of Presentation
      New Hampshire(アメリカ)
    • Year and Date
      2011-06-30
    • Related Report
      2011 Annual Research Report
  • [Presentation] V1-ATPaseの結晶構造から見えてきた回転メカニズム2011

    • Author(s)
      村田武士
    • Organizer
      第11回日本蛋白質科学会ワークショップ
    • Place of Presentation
      大阪
    • Year and Date
      2011-06-09
    • Related Report
      2013 Final Research Report
  • [Presentation] V1-ATPaseの結晶構造から見えてきた回転メカニズム2011

    • Author(s)
      村田武士
    • Organizer
      第11回日本蛋白質科学会
    • Place of Presentation
      阪急エキスポパーク(大阪府)(招待講演)
    • Year and Date
      2011-06-09
    • Related Report
      2011 Annual Research Report
  • [Book] 回転分子モーターの動作原理-F1モーターとV1モーターの違い-生物物理2014

    • Author(s)
      村田武士
    • Related Report
      2013 Final Research Report
  • [Book] Cell-free expression of protein complexes for structural biology, Methods Mol. Biol2014

    • Author(s)
      Takaho Terada, Takeshi Murata, Mikako Shirouzu and Shigeyuki Yokoyama
    • Related Report
      2013 Final Research Report
  • [Book] Cell-free expression of protein complexes for structural biology2014

    • Author(s)
      Takaho Terada, Takeshi Murata, Mikako Shirouzu and Shigeyuki Yokoyama
    • Publisher
      Methods Mol. Biol.
    • Related Report
      2013 Annual Research Report
  • [Book] 回転分子モーターの動作原理―F1モーターとV1モーターの違い―2014

    • Author(s)
      村田武士
    • Publisher
      生物物理
    • Related Report
      2013 Annual Research Report
  • [Book] V-ATPaseの分子メカニズム, 膜タンパク質構造研究2013

    • Author(s)
      水谷健二, 山本三沙岐, 村田武士
    • Publisher
      化学同人
    • Related Report
      2013 Final Research Report
  • [Book] 「膜タンパク質」の重要性とその構造が拓く未来, 膜タンパク質構造研究2013

    • Author(s)
      村田武士, 野村紀通, 小林拓也, 岩田想
    • Publisher
      化学同人
    • Related Report
      2013 Final Research Report
  • [Book] 骨粗しょう症に関与する分子モーターの回転メカニズムと創薬への取組み, アンチエイジングシリーズ3「骨研究最前線」2013

    • Author(s)
      水谷健二, 村田武士
    • Publisher
      NTS
    • Related Report
      2013 Final Research Report
  • [Book] 骨粗しょう症に関与する分子モーターの回転メカニズムと創薬への取組み2013

    • Author(s)
      水谷健二、村田武士
    • Publisher
      アンチエイジングシリーズ3「骨研究最前線」, NTS
    • Related Report
      2013 Annual Research Report
  • [Book] 「膜タンパク質」の重要性とその構造が拓く未来2013

    • Author(s)
      村田武士、野村紀通、小林拓也、岩田想
    • Publisher
      膜タンパク質構造研究, 化学同人
    • Related Report
      2013 Annual Research Report
  • [Book] V-ATPaseの分子メカニズム2013

    • Author(s)
      水谷健二、山本三沙岐、村田武士
    • Publisher
      膜タンパク質構造研究, 化学同人
    • Related Report
      2013 Annual Research Report
  • [Book] 抗体を用いた膜タンパク質の結晶構造解析, 新機能抗体開発ハンドブック2012

    • Author(s)
      日野智也, 岩田想, 村田武士
    • Publisher
      NTS
    • Related Report
      2013 Final Research Report
  • [Book] 抗体を用いた膜タンパク質の結晶構造解析2012

    • Author(s)
      日野智也
    • Total Pages
      5
    • Publisher
      NTS 新機能抗体開発ハンドブック
    • Related Report
      2012 Annual Research Report
  • [Remarks]

    • URL

      http://murata-lab.matrix.jp

    • Related Report
      2013 Final Research Report
  • [Remarks] 非対称な結晶構造から明らかになったV1-ATPaseの回転機構

    • URL

      http://first.lifesciencedb.jp/archives/6593

    • Related Report
      2012 Annual Research Report

URL: 

Published: 2011-04-06   Modified: 2023-03-16  

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