Structural physiology of the gastric proton pump

• Project/Area Number: 17H03653
• Research Category: Grant-in-Aid for Scientific Research (B)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Functional biochemistry
• Research Institution: Nagoya University
• Principal Investigator: Abe Kazuhiro 名古屋大学, 細胞生理学研究センター, 准教授 (60596188)
• Project Period (FY): 2017-04-01 – 2021-03-31
• Project Status: Completed (Fiscal Year 2020)
• Budget Amount: ¥17,030,000 (Direct Cost: ¥13,100,000、Indirect Cost: ¥3,930,000); Fiscal Year 2020: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000); Fiscal Year 2019: ¥2,990,000 (Direct Cost: ¥2,300,000、Indirect Cost: ¥690,000); Fiscal Year 2018: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2017: ¥5,980,000 (Direct Cost: ¥4,600,000、Indirect Cost: ¥1,380,000)
• Keywords: 機能生物化学 / 膜タンパク質 / P型ATPase / 胃プロトンポンプ / 胃 / X線結晶構造解析 / Cryo EM / 能動輸送体 / 構造生物学 / P-type ATPases / 蛋白質 / 構造解析 / P-type ATPase

Outline of Final Research Achievements

We determined high-resolution structures of the gastric proton pump, which provide molecular basis of how this pump acidify our gastric juice down to pH 1 (Abe et al., 2018, Nature). We also determined K+-bound form of the proton pump to show unequivocally its transport stoichiometry (Yamamoto et al., 2019, eLife).
We further determined crystal and cryoEM structures of phospholipid flippase, and revealed its molecular mechanisms.

Academic Significance and Societal Importance of the Research Achievements

少なくともヒトの組織において最大のイオン濃度勾配を作り出すことのできる胃プロトンポンプの最も重要なメカニズム『どのようにしてpH1もの強酸（胃酸）に対してH+を輸送することができるのかが明らかになった。
不快な胸焼けを伴う胃炎は、胃の中が強い酸性の為に引き起こされる。胃プロトンポンプの高分解能構造は、現在臨床利用される胃酸抑制剤の改良や、新たな作用機序をもった薬剤の論理的設計に資する。
脂質フリッパーゼの構造解析によって、イオンポンプと近縁のタンパク質でありながら、どのようにイオンと比して巨大な基質（リン脂質）を輸送できるのか、その分子メカニズムを明らかにした。

Research Products

• [Int'l Joint Research] University of southern Denmark(デンマーク)
• [Int'l Joint Research] University of Southern Denmark(デンマーク)
• [Journal Article] Crystal structure of a human plasma membrane phospholipid flippase (2020)
  • Author(s): Nakanishi Hanayo、Irie Katsumasa、Segawa Katsumori、Hasegawa Kazuya、Fujiyoshi Yoshinori、Nagata Shigekazu、Abe Kazuhiro
  • Journal Title: Journal of Biological Chemistry Volume: 295 Issue: 30 Pages: 10180-10194
  • DOI: 10.1074/jbc.ra120.014144
  • Peer Reviewed / Open Access
• [Journal Article] Transport Cycle of Plasma Membrane Flippase ATP11C by Cryo-EM (2020)
  • Author(s): Nakanishi Hanayo、Nishizawa Tomohiro、Segawa Katsumori、Nureki Osamu、Fujiyoshi Yoshinori、Nagata Shigekazu、Abe Kazuhiro
  • Journal Title: Cell Reports Volume: 32 Issue: 13 Pages: 108208-108208
  • DOI: 10.1016/j.celrep.2020.108208
  • Peer Reviewed / Open Access
• [Journal Article] Isoform-selective regulation of mammalian cryptochromes (2020)
  • Author(s): Miller Simon、Son You Lee、Aikawa Yoshiki、Makino Eri、Nagai Yoshiko、Srivastava Ashutosh、Oshima Tsuyoshi、Sugiyama Akiko、Hara Aya、Abe Kazuhiro、Hirata Kunio、Oishi Shinya、Hagihara Shinya、Sato Ayato、Tama Florence、Itami Kenichiro、Kay Steve A.、Hatori Megumi、Hirota Tsuyoshi
  • Journal Title: Nature Chemical Biology Volume: - Issue: 6 Pages: 676-685
  • DOI: 10.1038/s41589-020-0505-1
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] Isoform-selective regulation of mammalian cryptochromes (2020)
  • Author(s): Simon Miller, You Lee Son, Yoshiki Aikawa, Eri Makino, Yoshiko Nagai, Ashutosh Srivastava, Tsuyoshi Oshima, Akiko Sugiyama, Aya Hara, Kazuhiro Abe, Kunio Hirata, Shinya Oishi, Shinya Hagihara, Ayato Sato, Florence Tama, Kenichiro Itami, Steve A. Kay, Megumi Hatori & Tsuyoshi Hirota
  • Journal Title: Nat. Chem. Biol. Volume: in press
  • Peer Reviewed / Int'l Joint Research
• [Journal Article] A single K+-binding site in the crystal structure of the gastric proton pump (2019)
  • Author(s): Yamamoto Kenta、Dubey Vikas、Irie Katsumasa、Nakanishi Hanayo、Khandelia Himanshu、Fujiyoshi Yoshinori、Abe Kazuhiro
  • Journal Title: eLife Volume: 8
  • DOI: 10.7554/elife.47701
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Purified F-ATP synthase forms a Ca2+dependent high-conductance channel matching the mitochondrial permeability transition pore. (2019)
  • Author(s): Urbani A,Giorgio V,Carrer A, Franchin C,Arrigoni G, Jiko C,Abe K,Maeda S, Sginzawa-Itoh K, Bogers JF, McMillan DG, Gerle C, Szabo I, Bernardi P
  • Journal Title: Nature communications Volume: 4341 Issue: 1 Pages: 4341-4341
  • DOI: 10.1038/s41467-019-12331-1
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Crystal structures of the gastric proton pump (2018)
  • Author(s): Abe Kazuhiro、Irie Katsumasa、Nakanishi Hanayo、Suzuki Hiroshi、Fujiyoshi Yoshinori
  • Journal Title: Nature Volume: 556 Issue: 7700 Pages: 214-218
  • DOI: 10.1038/s41586-018-0003-8
  • Peer Reviewed
• [Journal Article] K+ binding and proton redistribution in the E2P state of the H+, K+-ATPase (2018)
  • Author(s): Dubey Vikas、Han Minwoo、Kopec Wojciech、Solov’yov Ilia A.、Abe Kazuhiro、Khandelia Himanshu
  • Journal Title: Scientific Reports Volume: 8 Issue: 1 Pages: 1-11
  • DOI: 10.1038/s41598-018-30885-w
• [Journal Article] The cryo-EM structure of gastric H+,K+-ATPase with bound BYK99, a high-affinity member of K+-competitive, imidazo[1,2-a]pyridine inhibitors (2017)
  • Author(s): Abe Kazuhiro、Shimokawa Jun、Naito Mao、Munson Keith、Vagin Olga、Sachs George、Suzuki Hiroshi、Tani Kazutoshi、Fujiyoshi Yoshinori
  • Journal Title: Scientific Reports Volume: 7 Issue: 1 Pages: 6632-6632
  • DOI: 10.1038/s41598-017-06698-8
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Presentation] 『細胞死を司るポンプ』脂質フリッパーゼATP11Cの結晶構造とCryoEM構造 (2020)
  • Author(s): 阿部一啓
  • Organizer: 日本生体エネルギー研究会
• [Presentation] 細胞膜フリッパーゼATP11Cの構造機能解析 (2020)
  • Author(s): 阿部一啓
  • Organizer: 第93回日本生化学会
• [Presentation] Crystal structures of the gastric proton pump - molecular basis for the binding of acid suppressants, H+-extrusion and K+-counter-transport (2020)
  • Author(s): Kazuhiro Abe
  • Organizer: 日本薬学会
  • Invited
• [Presentation] Structural basis of the proton extrusion mechanism of the gastric proton pump (2020)
  • Author(s): Kazuhiro Abe
  • Organizer: 第97回日本生理学会大会
  • Invited
• [Presentation] Molecular mechanisms for the drug binding, H+-extrusion and the K+ counter-transport (2019)
  • Author(s): Kazuhiro Abe
  • Organizer: Academia Sinica IBC seminar
  • Int'l Joint Research / Invited
• [Presentation] Crystal structure of the gastric proton pump (2019)
  • Author(s): Kazuhiro Abe
  • Organizer: World Laureates Forum 2nd conference
  • Int'l Joint Research / Invited
• [Presentation] X線結晶学とクライオ電顕で得られた構造情報の上手な活用法 ～胃プロトンポンプの構造解析を例として～ (2019)
  • Author(s): 阿部一啓
  • Organizer: 2019年度生理研研究会
  • Invited
• [Presentation] 胃プロトンポンプの輸送機構に対する構造基盤 (2019)
  • Author(s): Kazuhiro Abe
  • Organizer: 生物物理第57回年会 台湾‐日本 二国間シンポジウム：X線結晶構造解析とクライオ電顕2019
  • Invited
• [Presentation] Structural basis for the H+-extrusion and the K+-occlusion of the gastric proton pump (2019)
  • Author(s): Kazuhiro Abe
  • Organizer: Society of General Physiology /SOBLA 2019
  • Int'l Joint Research / Invited
• [Presentation] 胃の強酸性化の分子メカニズム ‐胃プロトンポンプの結晶構造解析 (2018)
  • Author(s): 阿部一啓
  • Organizer: 生体エネルギー研究会
  • Invited
• [Presentation] Crystal structures of the gastric proton pump (2018)
  • Author(s): Abe K
  • Organizer: AsCA
  • Int'l Joint Research / Invited
• [Presentation] 胃の強酸性化の秘密 (2018)
  • Author(s): 阿部一啓
  • Organizer: 創薬等ライフサイエンス研究支援基盤事業 平成30年度BINDS公開シンポジウム
  • Invited
• [Presentation] 胃プロトンポンプの結晶構造によって明らかになったH+排出機構 (2018)
  • Author(s): 阿部一啓
  • Organizer: 大阪大学蛋白質研究所セミナー
  • Invited
• [Presentation] Structural basis for the H+ extrusion and the transport stoichiometry of the gastric proton pump (2018)
  • Author(s): Abe K
  • Organizer: Frontiers in P-type ATPase Research 2018
  • Int'l Joint Research / Invited
• [Presentation] Structural and functional analysis of gastric H+,K+-ATPase (2017)
  • Author(s): Abe K.
  • Organizer: The 15th international conference on Na,K-ATPase and related transport ATPases
  • Int'l Joint Research / Invited
• [Presentation] Structural and functional analysis of gastric proton pump and acid suppressants (2017)
  • Author(s): Abe K.
  • Organizer: ConBio2017
  • Int'l Joint Research / Invited
• [Remarks] 細胞生理学研究センター
  • URL: http://www.cespi.nagoya-u.ac.jp/BasicBiol/kabe/2018_HP_Abe.pdf