Structural biology of secondary active transporters

• Project/Area Number: 22687007
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Structural biochemistry
• Research Institution: The University of Tokyo
• Principal Investigator: ISHITANI Ryuichiro 東京大学, 大学院・理学系研究科, 准教授 (90361568)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥25,610,000 (Direct Cost: ¥19,700,000、Indirect Cost: ¥5,910,000); Fiscal Year 2012: ¥7,670,000 (Direct Cost: ¥5,900,000、Indirect Cost: ¥1,770,000); Fiscal Year 2011: ¥8,580,000 (Direct Cost: ¥6,600,000、Indirect Cost: ¥1,980,000); Fiscal Year 2010: ¥9,360,000 (Direct Cost: ¥7,200,000、Indirect Cost: ¥2,160,000)
• Keywords: X 線結晶構造解析 / 膜蛋白質 / 膜輸送体 / ドラッグデリバリー / 多剤排出因子 / X線結晶構造解析

Research Abstract

Active transporters are membrane protein that mediates translocation of various substrates across the biological membrane by consuming energy, and thus are important for maintaining intra- and extracellular environment. The secondary active transporters translocate the small molecules, including amino acids, nucleic acids, sugars and drags,by utilizing the electrochemical gradient of H+ or Na+ across the membrane. In this project, we focused on the three important secondary active transporters, multidrug efflux transporter MATE, Ca2+/cation exchanger CaCA, and oligopeptide symporter POT, and performed structural and functional analyses of these targets.

Research Products

• [Journal Article] Structural Basis for the Counter-Transport Mechanism of a H+/Ca2+ Exchanger. (2013)
  • Author(s): Nishizawa T, Kita S, Maturana AD,Furuya N, Hirata K, Kasuya G, Ogasawara S,Dohmae N, Iwamoto T, Ishitani R, NurekiO.
  • Journal Title: Science Volume: (掲載決定)
  • Peer Reviewed
• [Journal Article] Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT. (2013)
  • Author(s): Doki S, Kato HE, Solcan N, Iwaki M, Koyama M, Iwase N, Tsukazaki T, Hattori M, Sugita Y, Kandori H, Newstead S, Ishitani R ,Nureki O.
  • Journal Title: Proc Natl Acad Sci USA Volume: (掲載決定)
  • Peer Reviewed
• [Journal Article] Screening and X-Ray Crystal Structure-based Optimization of Autotaxin (ENPP2) Inhibitors, Using a Newly Developed Fluorescence Probe. (2013)
  • Author(s): Kawaguchi M, Okabe T, Okudaira S, Nishimasu H, Ishitani R, Kojima H, Nureki O, Aoki J, Nagano T.
  • Journal Title: ACS Chem Biol Volume: (掲載決定)
  • Peer Reviewed
• [Journal Article] Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. (2013)
  • Author(s): Tanaka Y, Hipolito CJ, Maturana AD, Ito K, Kuroda T, Higuchi T, Katoh T, Kato HE, Hattori M, Kumazaki K, Tsukazaki T, Ishitani R, Suga H, Nureki O.
  • Journal Title: Nature Volume: 496 Pages: 247-251
  • Peer Reviewed
• [Journal Article] Crystal structure of Cex1p reveals the mechanism of tRNA trafficking between nucleus and cytoplasm (2013)
  • Author(s): Nozawa K, Ishitani R, Yoshihisa T, Sato M, Arisaka F, Kanamaru S, Dohmae N, Mangroo D, Senger B, Becker HD, Nureki O
  • Journal Title: Nucleic Acids Res Volume: 41 Pages: 3901-3901
  • Peer Reviewed
• [Journal Article] Structure and function of Zucchini endoribonuclease in piRNA biogenesis (2013)
  • Author(s): Y. Tanaka, C. J. Hipolito, A. D. Maturana, K. Ito, T. Kuroda, T. Higuchi, T. Katoh, H. E. Kato, M. Hattori, K. Kumazaki, T. Tsukazaki, R. Ishitani, H. Suga and O. Nureki
  • Journal Title: Nature Volume: 496 Pages: 284-284
  • DOI: 10.1038/nature11509
  • Peer Reviewed
• [Journal Article] Backbone resonance assignments for the cytoplasmic region of the Mg^<2+> transporter MgtE in the Mg^<2+>-unbound state (2013)
  • Author(s): Maruyama T, Imai S, Osawa M, Hattori M, Ishitani R, Nureki O, Shimada I.
  • Journal Title: Biomol NMR Assign. Volume: 7 Pages: 93-6
  • DOI: 10.1007/s12104-012-9385-y
  • Peer Reviewed
• [Journal Article] Structure and function of Zucchini endoribonuclease in piRNA biogenesis. (2012)
  • Author(s): Nishimasu H, Ishizu H, Saito K, Fukuhara S, Kamatani MK, Bonnefond L, Matsumoto N, Nishizawa T, Nakanaga K, Aoki J, Ishitani R, Siomi H, Siomi MC, Nureki O.
  • Journal Title: Nature Volume: 491 Pages: 284-287
  • Peer Reviewed
• [Journal Article] Molecular Dynamics Simulation of Autotaxin: Roles of the Nuclease-like Domain and the Glycan Modification. (2012)
  • Author(s): Koyama M, Nishimasu H, Ishitani R , Nureki O.
  • Journal Title: J Phys Chem B Volume: 116 Pages: 11798-11808
  • Peer Reviewed
• [Journal Article] Structural basis for trans lation termination by archaeal RF1 and GTP-bound EF1α complex. (2012)
  • Author(s): Kobayashi K, Saito K, Ishitani R , Ito K, Nureki O.
  • Journal Title: Nucleic Acids Res Volume: 40 Pages: 9319-9328
  • Peer Reviewed
• [Journal Article] Spatial distribution of cytoplasmic domains of the Mg2+-transporter MgtE, in a solution lacking Mg2+, revealed by paramagnetic relaxation enhancement. (2012)
  • Author(s): Imai S, Maruyama T, Osawa M, Hattori M, Ishitani R, Nureki O, Shimada I.
  • Journal Title: Biochim Biophys Acta Volume: 1824 Pages: 1129-1135
  • Peer Reviewed
• [Journal Article] Crystal structure of the channelrhodopsin light-gated cation channel. (2012)
  • Author(s): Kato HE, Zhang F, Yizhar O, RamakrishnanC, Nishizawa T, Hirata K, Ito J, Aita Y, Tsukazaki T, Hayashi S, Hegemann P, Maturana AD, Ishitani R, Deisseroth K, Nureki O.
  • Journal Title: Nature Volume: 482 Pages: 369-374
  • Peer Reviewed
• [Journal Article] Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Zucchini from Drosophila melanogaster (2012)
  • Author(s): Fukuhara S, Nishimasu H, Bonnefond L, Matsumoto N, Ishitani R, Nureki O
  • Journal Title: Acta Crystallogr Sect F Struct Biol Cryst Commun Volume: F68 Pages: 1346-1346
  • DOI: 10.1107/s1744309112038936
  • Peer Reviewed
• [Journal Article] The tRNA recognition mechanism of folate/FAD-dependent tRNA methyltransferase (TrmFO). (2012)
  • Author(s): Yamagami R, Yamashita K, Nishimasu H, Tomikawa C, Ochi A, Iwashita C, Hirata A, Ishitani R, Nureki O, Hori H
  • Journal Title: Journal of Biological Chemistry Volume: 287 Pages: 42480-42480
  • DOI: 10.1074/jbc.m112.390112
  • Peer Reviewed
• [Journal Article] Specific recognition of linear polyubiquitin by A20 zinc finger 7 is involved in NF-κB regulation. (2012)
  • Author(s): Tokunaga F, Nishimasu H, Ishitani R, Goto E, Noguchi T, Mio K, Kamei K, Ma A, Iwai K, Nureki O
  • Journal Title: EMBO J Volume: 31 Pages: 3856-3856
  • DOI: 10.1038/emboj.2012.241
  • Peer Reviewed
• [Journal Article] Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin (2012)
  • Author(s): Kato K, Nishimasu H, Okudaira S, Mihara E, Ishitani R, Takagi J, Aoki J, Nureki O
  • Journal Title: Proc Natl Acad Sci USA Volume: 109 Pages: 16876-16876
  • DOI: 10.1073/pnas.1208017109
  • Peer Reviewed
• [Journal Article] Molecular dynamics simulation of Autotaxin : roles of the nuclease-like domain and the glycan modification (2012)
  • Author(s): Michio Koyama, Hiroshi Nishimasu, Ryuichiro Ishitani, Osamu Nureki
  • Journal Title: J Phys Chem B Volume: 116 Pages: 11798-11798
  • DOI: 10.1021/jp303198u
  • Peer Reviewed
• [Journal Article] Simplification of the genetic code: restricted diversity of genetically encoded amino acids (2012)
  • Author(s): Kawahara-Kobayashi A, Masuda A, Araiso Y, Sakai Y, Kohda A, Uchiyama M, Asami S, Matsuda T, Ishitani R, Dohmae N, Yokoyama S, Kigawa T, Nureki O, Kiga D
  • Journal Title: Nucleic Acids Research Volume: 40 Pages: 10576-10576
  • DOI: 10.1093/nar/gks786
  • Peer Reviewed
• [Journal Article] Structural basis for translation termination by archaeal RF1 an GTP-bound EF1α complex. (2012)
  • Author(s): Kan Kobayashi, Kazuki Saito, Ryuichiro Ishitani, Koichi Ito, Osamu Nureki
  • Journal Title: Nucleic Acids Res Volume: 40 Pages: 9319-28
  • DOI: 10.1093/nar/gks660
  • Peer Reviewed
• [Journal Article] Expression, purification, crystallization and preliminary X-ray crystallographic analysis of Enpp1 (2012)
  • Author(s): Kato K, Nishimasu H, Mihara E, Ishitani R, Takagi J, Aoki J, Nureki O
  • Journal Title: Acta Crystallographica Section F Volume: F68 Pages: 778-778
  • DOI: 10.1107/s1744309112019306
  • Peer Reviewed
• [Journal Article] Spatial distribution of cytoplasmic domains of the Mg(2+)-transporter MgtE, in a solution lacking Mg(2+), revealed by paramagnetic relaxation enhancement. (2012)
  • Author(s): Imai S, Maruyama T, Osawa M, Hattori M, Ishitani R, Nureki O, Shimada I.
  • Journal Title: Biochim Biophys Acta. Volume: 1824 Pages: 1129-1129
  • DOI: 10.1016/j.bbapap.2012.06.008
  • Peer Reviewed
• [Journal Article] Structure of a dominant-negative helix-loop-helix tran- scriptional regulator suggests mechanisms of autoinhibition (2012)
  • Author(s): Ishii R
  • Journal Title: EMBO J. Volume: 31 Pages: 2541-2552
  • DOI: 10.1038/emboj.2012.77
  • Peer Reviewed
• [Journal Article] A 3D view of autotaxin (2012)
  • Author(s): Nishimasu H, Ishitani R, Aoki J, Nureki O
  • Journal Title: Trends Pharmacol Sci. Volume: 33 Pages: 138-145
  • DOI: 10.1016/j.tips.2011.12.004
  • Peer Reviewed
• [Journal Article] Crystal structure of the channelrhodops in light-gated cation channel (2012)
  • Author(s): Hideaki E.Kato, Feng Zhang, Ofer Yizhar, Charu Ramakrishnan, Tomohiro Nishizawa, Kunio Hirata, Jumpei Ito, Yusuke Aita, Tomoya Tsukazaki, Shigehiko Hayashi, Peter Hegemann, Andres D.Maturana, Ryuichiro Ishitani, Karl Deisseroth, Osamu Nureki
  • Journal Title: Nature Volume: 482 Pages: 369-374
  • DOI: 10.1038/nature10870
  • Peer Reviewed
• [Journal Article] Crystallization and preliminary X-ray diffraction of the first periplasmic domain of SecDF, a translocon-associated membrane protein, from Thermus thermophilus (2011)
  • Author(s): Echizen Y, Tsukazaki T, Dohmae N, Ishitani R, Nureki O
  • Journal Title: Acta Cryst. Volume: F67 Pages: 376-380
  • DOI: 10.1107/s1744309106007779
  • Peer Reviewed
• [Journal Article] Structure and function of a membrane component SecDF that enhances protein exportStructure and function of a membrane component SecDF that enhances protein export. (2011)
  • Author(s): Tsukazaki, T., et al
  • Journal Title: Nature Volume: 475 Pages: 235-238
  • DOI: 10.1038/nature09980
  • Peer Reviewed
• [Journal Article] Crystal structure of autotaxin and insight into GPCR activation by lipid mediators (2011)
  • Author(s): Nishimasu H, (他), Ishitani R, Takagi J, Aoki J, Nureki O
  • Journal Title: Proc Natl Acad Sci USA Volume: 18 Pages: 205-212
  • Peer Reviewed
• [Journal Article] Structural basis for nonribosomal peptide synthesis by an aminoacyl-tRNA synthetase paralog (2011)
  • Author(s): Bonnefond L, (他), Ishitani R, Nureki O.
  • Journal Title: Proc Natl Acad Sci USA Volume: 108 Pages: 3912-3917
  • Peer Reviewed
• [Journal Article] Crystal structure of a novel JmjC-domain-containing protein, TYW5, involved in tRNA modification (2011)
  • Author(s): Kato M, (他), Ishitani R, Nureki O
  • Journal Title: Nucleic Acids Res Volume: (未定)
  • Peer Reviewed
• [Journal Article] C-terminal domain of archaeal O-phosphoseryl-tRNA kinase displays large-scale motion to bind the 7-bp D-stem of archaeal tRNASec (2011)
  • Author(s): Sherrer RL, (他) Ishitani R, Ho JM, Soll D, Nureki O
  • Journal Title: Nucleic Acids Res Volume: (未定)
  • Peer Reviewed
• [Journal Article] Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex (2010)
  • Author(s): Kobayashi K, (他), Ishitani R, Inada T, Nureki O
  • Journal Title: Proc Natl Acad Sci USA Volume: 107 Pages: 17575-17579
  • Peer Reviewed
• [Journal Article] Omnipotent role of archaeal elongation factor 1 alpha (EF1α) in translational elongation and termination, and quality control of protein synthesis. (2010)
  • Author(s): Saito K, Kobayashi K, (他), Ishitani R, Nureki O, Ito K
  • Journal Title: Proc Natl Acad Sci USA Volume: 107 Pages: 19242-19247
  • Peer Reviewed
• [Journal Article] Expanding role of the Jumonji C domain as an RNA hydroxylase (2010)
  • Author(s): Noma A, Ishitani R, Kato M, Nagao A, Nureki O, Suzuki T
  • Journal Title: J Biol Chem Volume: 285 Pages: 34503-7
  • Peer Reviewed
• [Journal Article] Structure of an archaeal non-discriminating glutamyl-tRNA synthetase : a missing link in the evolution of Gln-tRNAGln formation (2010)
  • Author(s): Nureki O, (他), Ishitani R
  • Journal Title: Nucleic Acids Res Volume: 38 Pages: 7286-7297
  • Peer Reviewed
• [Journal Article] Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon (2010)
  • Author(s): Mori T, Ishitani R, Tsukazaki T, Nureki O, Sugita Y
  • Journal Title: Biochemistry Volume: 49 Pages: 945-950
  • Peer Reviewed
• [Presentation] Structural basis for mRNA surveillance by archaeal Pelota and GTP-bound EF1α complex (2012)
  • Author(s): 石谷隆一郎
  • Organizer: XXIV tRNA Conference
  • Place of Presentation: Olmue, Chile
• [Presentation] Structural basis forH+-coupled symport mechanism by POT (2012)
  • Author(s): 石谷隆一郎
  • Organizer: GRCon Membrane Transport Proteins
  • Place of Presentation: Les Diablerets Conference Center, Les Diablerets, Switzerland
• [Presentation] Structural basis for H+-coupled symport mechanism by POT (2012)
  • Author(s): 石谷隆一郎
  • Organizer: GRC on Membrane Transport Proteins
  • Place of Presentation: Les Diablerets Conference Center, Les Diablerets, Switzerland
• [Presentation] 結晶構造解析と分子動力学シミュレーションから調べるタンパク質のダイナミクス (2012)
  • Author(s): 石谷隆一郎
  • Organizer: JSIAM2012
  • Place of Presentation: 稚内
  • Year and Date: 2012-08-30
• [Presentation] Structure of a dominant-negative helix-loop-helix transcriptional regulator suggests mechanisms of autoinhibition (2011)
  • Author(s): 石谷隆一郎
  • Organizer: 分子生物学会年会
  • Place of Presentation: パシフィコ横浜(招待講演)
  • Year and Date: 2011-12-16
• [Presentation] 古細菌由来Pelota・EF1α・GTP複合体によるmRNA品質管理機構の構造基盤 (2010)
  • Author(s): 石谷隆一郎
  • Organizer: 日本分子生物学会年会
  • Place of Presentation: 神戸ポートアイランド
  • Year and Date: 2010-12-07
• [Book] 酵素利用技術大系-基礎・解析から改変・高機能化・産業利用まで-(1章1節2) (2010)
  • Author(s): 石谷隆一郎、荒磯裕平、野澤佳世
  • Total Pages: 800
  • Publisher: エヌ・ティー・エス
• [Remarks]
  • URL: http://www.nurekilab.net/
• [Remarks] 濡木研究室
  • URL: http://www.nurekilab.net/
• [Remarks]
  • URL: http://www.nurekilab.net/