Structural biology of multidrug transporters

2016 Fiscal Year Annual Research Report

• Project/Area Number: 25291011
• Research Institution: The University of Tokyo
• Principal Investigator: 石谷 隆一郎 東京大学, 理学(系)研究科(研究院), 准教授 (90361568)
• Project Period (FY): 2013-04-01 – 2017-03-31
• Keywords: Ｘ線結晶構造解析 / 膜タンパク質 / 多剤耐性菌 / 薬物動態

Outline of Annual Research Achievements

Drug/Metabolite Transporter (DMT)は真正細菌、古細菌から真核生物に至るまで広く保存された膜輸送体のスーパーファミリーであり、毒物や代謝産物など様々な低分子化合物の輸送に関与している。DMTに属する輸送体であるYddGは，アミノ酸等を細胞外へと排出することで細胞内の代謝物恒常性に関わっており，真正細菌の間で広く保存されている。我々は、細菌Starkeya novella由来YddGの立体構造を2.4Å分解能で決定した。その結果、YddGは従来の輸送体ファミリーには見られない新規な折り畳みを持つ膜蛋白質であることが判明した．分子中央部には大きなポケットが形成されており、ポケット内部をアミノ酸分子が入りやすい容積や環境にすることで、基質アミノ酸や薬剤とそれ以外の物質を選択し、細胞外へ排出することが判明した。さらに、構造情報に基づく生化学的解析とMDシミュレーションから、YddGが基質を輸送するメカニズムは、これまで類似の報告が無い新規のものであることが明らかになった。以上の結果はNature誌に掲載された．真核生物由来MATEに関しては，構造解析可能なレベルの量・純度・安定性を有する真核生物由来MATE 発現系の網羅的探索を行ったところ，ひとつの系について有望な候補が見つかった．現在，後続のプロジェクトとして採択された基盤(B) 17H03640のサポートにより引き続き大量調製，結晶化と構造解析を推進している．

Research Progress Status

28年度が最終年度であるため、記入しない。

Strategy for Future Research Activity

28年度が最終年度であるため、記入しない。

Research Products

• [Journal Article] Crystal structures of the TRIC trimeric intracellular cation channel orthologues (2016)
  • Author(s): Kasuya G, Hiraizumi M, Maturana AD, Kumazaki K, Fujiwara Y, Liu K, Nakada-Nakura Y, Iwata S, Tsukada K, Komori T, Uemura S, Goto Y, Nakane T, Takemoto M, Kato HE, Yamashita K, Wada M, Ito K, Ishitani R, Hattori M, Nureki O
  • Journal Title: Cell Res. Volume: 26 Pages: 1288-1301
  • DOI: 10.1038/cr.2016.140
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structural and Functional Analysis of DDX41: a bispecific immune receptor for DNA and cyclic dinucleotide (2016)
  • Author(s): Omura H, Oikawa D, Nakane T, Kato M, Ishii R, Ishitani R, Tokunaga F, Nureki O
  • Journal Title: Sci Rep. Volume: 6 Pages: 34756
  • DOI: 10.1038/srep34756
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Crystal Structure of Silkworm PIWI-Clade Argonaute Siwi Bound to piRNA (2016)
  • Author(s): Matsumoto N, Nishimasu H, Sakakibara K, Nishida KM, Hirano T, Ishitani R, Siomi H, Siomi MC, Nureki O
  • Journal Title: Cell Volume: 167 Pages: 484-497
  • DOI: 10.1016/j.cell.2016.09.002
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Breakpoint Cluster Region-Mediated Inflammation Is Dependent on Casein Kinase II (2016)
  • Author(s): Meng J, Jiang JJ, Atsumi T, Bando H, Okuyama Y, Sabharwal L, Nakagawa I, Higuchi H, Ota M, Okawara M, Ishitani R, Nureki O, Higo D, Arima Y, Ogura H, Kamimura D, Murakami M
  • Journal Title: J Immunol. Volume: 197 Pages: 3111-3119
  • DOI: 10.4049/jimmunol.1601082
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Linear ubiquitination is involved in the pathogenesis of optineurin-associated amyotrophic lateral sclerosis (2016)
  • Author(s): Nakazawa S, Oikawa D, Ishii R, Ayaki T, Takahashi H, Takeda H, Ishitani R, Kamei K, Takeyoshi I, Kawakami H, Iwai K, Hatada I, Sawasaki T, Ito H, Nureki O, Tokunaga F
  • Journal Title: Nat. Commun. Volume: 7 Pages: 12547
  • DOI: 10.1038/ncomms12547
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Crystal structure of the plant receptor-like kinase TDR in complex with the TDIF peptide (2016)
  • Author(s): Morita J, Kato K, Nakane T, Kondo Y, Fukuda H, Nishimasu H, Ishitani R, Nureki O
  • Journal Title: Nat Commun Volume: 7 Pages: 12383
  • DOI: 10.1038/ncomms12383
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structural and functional insights into IZUMO1 recognition by JUNO in mammalian fertilization (2016)
  • Author(s): Kato K, Satouh Y, Nishimasu H, Kurabayashi A, Morita J, Fujihara Y, Oji A, Ishitani R, Ikawa M, Nureki O
  • Journal Title: Nat Commun Volume: 7 Pages: 12198
  • DOI: 10.1038/ncomms12198
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae (2016)
  • Author(s): Kusakizako T, Tanaka Y, Hipolito CJ, Kuroda T, Ishitani R, Suga H, Nureki O
  • Journal Title: Acta Crystallogr F Struct Biol Commun Volume: 72 Pages: 552-557
  • DOI: 10.1107/S2053230X16008931
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structural basis for amino acid export by DMT superfamily transporter YddG (2016)
  • Author(s): Tsuchiya H, Doki S, Takemoto M, Ikuta T, Higuchi T, Fukui K, Usuda Y, Tabuchi E, Nagatoishi S, Tsumoto K, Nishizawa T, Ito K, Dohmae N, Ishitani R, Nureki O
  • Journal Title: Nature Volume: 534 Pages: 417-420
  • DOI: 10.1038/nature17991
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Data processing pipeline for serial femtosecond crystallography at SACLA (2016)
  • Author(s): Nakane T, Joti Y, Tono K, Yabashi M, Nango E, Iwata S, Ishitani R, Nureki O
  • Journal Title: J Appl Crystallogr Volume: 49 Pages: 1035-1041
  • DOI: 10.1107/S1600576716005720
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA (2016)
  • Author(s): Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O
  • Journal Title: Cell Volume: 165 Pages: 949-962
  • DOI: 10.1016/j.cell.2016.04.003
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structural basis for specific inhibition of Autotaxin by a DNA aptamer (2016)
  • Author(s): Kato K, Ikeda H, Miyakawa S, Futakawa S, Nonaka Y, Fujiwara M, Okudaira S, Kano K, Aoki J, Morita J, Ishitani R, Nishimasu H, Nakamura Y, Nureki O
  • Journal Title: Nat Struct Mol Biol Volume: 23 Pages: 395-401
  • DOI: 10.1038/nsmb.3200
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Mechanisms for Two-Step Proton Transfer Reactions in the Outward-Facing Form of MATE Transporter (2016)
  • Author(s): Nishima W, Mizukami W, Tanaka Y, Ishitani R, Nureki O, Sugita Y
  • Journal Title: Biophys J Volume: 110 Pages: 1346-1354
  • DOI: 10.1016/j.bpj.2016.01.027
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9 (2016)
  • Author(s): Hirano S, Nishimasu H, Ishitani R, Nureki O
  • Journal Title: Mol Cell Volume: 61 Pages: 886-894
  • DOI: 10.1016/j.molcel.2016.02.018
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Presentation] 膜輸送体の分子メカニズム (2016)
  • Author(s): 石谷隆一郎
  • Organizer: 分子生物学会第３９回年会
  • Place of Presentation: パシフィコ横浜（神奈川県横浜市）
  • Year and Date: 2016-11-30 – 2016-11-30
  • Int'l Joint Research / Invited
• [Presentation] Structural basis for amino acid export by DMT superfamily transporter YddG (2016)
  • Author(s): Ryuichiro Ishitani
  • Organizer: GRC Membrane Transport Proteins
  • Place of Presentation: Lucca (Barga), Italy
  • Year and Date: 2016-06-12 – 2016-06-17
  • Int'l Joint Research