People

Professor
Tomoya Tsukazaki

  • Hometown：Sayo-cho, Hyogo, Japan
  • Research Field：Structural Life Science
  • One of my favorites : Training
  • Special Skill: Experiment
  • Comment: We would like to present convincing results.

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Education, Research career

  • 2006　Graduate School of Science, Kyoto University, Work supervised by Professor Koreaki Ito
  • 2006　Ph.D. in science
  • 2006-2008　Post-Doctoral Fellow, Department of Biological Information, Tokyo Institute of Technology
  • 2008-2010　Assistant Professor, The institute of Medical Science, The university of Tokyo
  • 2010-2013　Assistant Professor, Graduate School of Science, The university of TokyoWork supervised by Professor Osamu Nureki (2006-2013)
  • 2012.10-2016.03　JST PRESTO Researcher (concurrent)
  • 2013.4-2018.7　Associate Professor, Nara Institute of Science and Technology
  • 2018.8-present Professor, Nara Institute of Science and Technology

Key Publications

  1. Tanaka Y, Yoshikaie K, Takeuchi A, Ichikawa M, Mori T, Uchino S, Sugano Y, Hakoshima T, Takagi H, Nonaka G and *Tsukazaki T.  Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake.  Sci. Adv. 8, eaba7637 (2020)

  2. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto VY, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y and *Tsukazaki T. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF Cell Rep. 19, 895-901 (2017).
  3. Tanaka Y, Sugano Y, Takemoto M, Mori T, Furukawa A, Kusakizako T, Kumazaki K, Kashima A, Ishitani R, Sugita Y, *Nureki O and *Tsukazaki T. Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State Cell Rep. 13, 1561-1568 (2015).
  4. Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, *Tsukazaki T and *Nureki O. Structural basis of Sec-independent membrane protein insertion by YidC. Nature 509, 516-520(2014).
  5. Tsukazaki T, Mori H, Echizen Y, Ishitani R, Fukai S, Tanaka T, Perederina A, Vassylyev DG, Kohno T, Maturana AD, Ito K and Nureki O. Structure and function of a membrane component SecDF that enhances protein export. Nature 474, 235-238 (2011).
  6. Tsukazaki T, Mori H, Fukai S, Ishitani R, Mori T, Dohmae N, Perederina A, Sugita Y, Vassylyev DG, Ito K and Nureki O. Conformational transition of Sec machinery inferred from bacterial SecYE structures. Nature 455, 988-991 (2008).

Awards

  • 2024

    Award for securing significant external funds (NAIST)

  • 2023

    Award for securing significant external funds (NAIST)

  • 2022

    Award for securing significant external funds (NAIST)

  • 2021

    Award for securing significant external funds (NAIST)

  • 2019

    Award for securing significant external funds (NAIST)

  • 2018

    Award for securing significant external funds (NAIST)

  • 2017

    Award for securing significant external funds (NAIST)

  • 2016

    Award for securing significant external funds (NAIST)

  • 2015

    Award for securing significant external funds (NAIST)

  • 2014

    Award for securing significant external funds (NAIST)

  • 2012

    The Young Scientists' Prize (MEXT)

  • 2010

    Early Research in Biophysics Award (Biophysical Society of Japan)

  • 2009

    Young Scientist Award (PSSJ)

Publications

  1. Ikeda Y, Miyazaki R, Tsukazaki T, Akiyama Y and *Mori H.  Translation arrest cancellation of VemP, a secretion monitor in Vibrio, is regulated by multiple cis and trans factors, including SecY. J. Biol. Chem.  300, 107735 (2024)

  2. Ikei M, Miyazaki R, Monden K, Naito Y, Takeuchi A, Takahashi YS, Tanaka Y, Mori T, *Ichikawa M and *Tsukazaki T.  YeeD is an essential partner for YeeE-mediated thiosulfate uptake in bacteria and regulates thiosulfate ion decomposition. PLoS Biol.  22, e3002601 (2024)

  3. Sato Y, Hashimoto T, Kato K, Okamura A, Hasegawa K, Shinone T, Tanaka Y, Tanaka Y, Tsukazaki T, Tsukamoto T, Demura M, Yao M and Kikukawa T.  Multistep conformational changes leading to the gate opening of light-driven sodium pump rhodopsin. J. Biol. Chem.  299, 105393 (2023)

  4. *Kohga H, Lertpreedakorn N, Miyazaki R and *Tsukazaki T.  Critical residues of the antibiotic peptide LysM that inhibits lipid II flipping.  bioRxiv  2023.05.22.541694 (2023)

  5. Miyazaki R, Ai M, Tanaka N, Suzuki T, Dhomae N, Tsukazaki T, Akiyama Y and *Mori H.  Inner membrane YfgM-PpiD heterodimer acts as a functional unit that associates with the SecY/E/G translocon and promotes protein translocation.  J. Biol. Chem. 298, 102572 (2022)

  6. *Inaba H, Sueki Y, Ichikawa M, Kabir AMR, Iwasaki T, Shigematsu H, Kakugo A, Sada K, Tsukazaki T and *Matsuura K.  Generation of stable microtubule superstructures by binding of peptide-fused tetrameric proteins to inside and outside.  Sci. Adv. 8, eabq3817 (2022) 

  7. Kohga H, Mori T, Tanaka Y, Yoshikaie K, Taniguchi K, Fujimoto K, Fritz L, Schneider T and *Tsukazaki T.  Crystal structure of the lipid flippase MurJ in a "squeezed" form distinct from its inward- and outward-facing forms.  Structure 30, 1088-1097 (2022)

  8. Tanaka Y, Iwaki S, Sasaki A and *Tsukazaki T.  Crystal structures of a nicotine MATE transporter provide insight into its mechanism of substrate transport.  FEBS Letters 595, 1902-1913 (2021)

  9. Daimon Y, Narita S, Miyazaki R, Hizukuri Y, Mori H, Tanaka Y, Tsukazaki T and *Akiyama Y. Reversible autoinhibitory regulation of Escherichia coli metallopeptidase BepA for selective β-barrel protein degradation. Proc. Natl. Acad. Sci. USA 117, 27989-27996 (2020)

  10. Tanaka Y, Yoshikaie K, Takeuchi A, Ichikawa M, Mori T, Uchino S, Sugano Y, Hakoshima T, Takagi H, Nonaka G and *Tsukazaki T.  Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake. Sci. Adv. 6, eaba7637 (2020)

  11. Sasaki M, Nishikawa H, Suzuki S, Moser M, Huber M, Sawasato K, Matsubayashi H, Kumazaki K, Tsukazaki T, Kuruma Y, Nureki O, Ueda T and Nishiyama KI.  The bacterial protein YidC accelerates MPIase-dependent integration of membrane proteins.  J. Biol. Chem. 294, 18898-18908 (2019)

  12. Tanaka Y and Tsukazaki T. A snapshot of membrane protein insertion. EMBO Rep. 20, e49034 (2019)

  13. Tsukazaki T. Structural Basis of the Sec Translocon and YidC Revealed Through X-ray Crystallography. The Protein Journal 38, 249-261 (2019)

  14. Inoue M, Sakuta N, Watanabe A, Zhang Y, Yoshikaie K, Tanaka Y, Ushioda R, Kato Y, Takagi J, Tsukazaki T, Nagata K and *Inaba K. Structural Basis of Sarco/Endoplasmic Reticulum Ca2+-ATPase 2b Regulation via Transmembrane Helix Interplay. Cell Rep. 27, 1221–1230 (2019)

  15. Shahrizal M, Daimon Y, Tanaka Y, Hayashi Y, Nakayama S, Iwaki S, Narita S, Kamikubo H, *Akiyama Y and *Tsukazaki T. Structural Basis for the Function of the β-Barrel Assembly-Enhancing Protease BepA.  J. Mol. Biol. 431, 625-635 (2019)

  16. Haruyama T, Sugano Y, Kodera N, Uchihashi T, Ando T, Tanaka Y, Konno H and *Tsukazaki T. Single-unit imaging of membrane protein-embedded nanodiscs from two oriented sides by high-speed atomic force microscopy. Structure 27, 152-160 (2019)

  17. Tanaka Y,  Izumioka A, Abdul HA, Fujii A, Haruyama T, Furukawa A and *Tsukazaki T.  2.8-Å crystal structure of Escherichia coli YidC revealing all core regions, including flexible C2 loop. Biochem. Biophys. Res. Commun. 505, 141-145 (2018)

  18. *Tsukazaki T.  Structure-based working model of SecDF, a proton-driven bacterial protein translocation factor. FEMS Microbiology Letters365, fny112 (2018)

  19. Furukawa A, Nakayama S, Yoshikaie K, Tanaka Y and *Tsukazaki T. Remote Coupled Drastic β-Barrel to β-Sheet Transition of the Protein Translocation Motor. Structure  26, 485–489 (2018)

  20. Daimon Y, Iwama-Masui C, Tanaka Y, Shiota T, Suzuki T, Miyazaki R, Sakurada H, Lithgow T, Dohmae N, Mori H, *Tsukazaki T, *Narita S and *Akiyama Y. The TPR domain of BepA is required for productive interaction with substrate proteins and the β-barrel assembly machinery complex. Mol. Microbiol. 106, 760-776 (2017).
  21. Furukawa A, Yoshikaie K, Mori T, Mori H, Morimoto VY, Sugano Y, Iwaki S, Minamino T, Sugita Y, Tanaka Y and *Tsukazaki T. Tunnel Formation Inferred from the I-Form Structures of the Proton-Driven Protein Secretion Motor SecDF. Cell Rep. 19, 895-901 (2017).
  22. Tanaka Y, Iwaki S and *Tsukazaki T.  Crystal Structure of a Plant Multidrug and Toxic Compound Extrusion Family Protein. Structure 25, 1455-1460 (2017).
  23. Sugano Y, Furukawa A, Nureki O, Tanaka Y and *Tsukazaki T. SecY-SecA fusion protein retains the ability to mediate protein transport.  PLOS ONE 12, e0183434 (2017)
  24. Tanaka Y, Sugano Y, Takemoto M, Mori T, Furukawa A, Kusakizako T, Kumazaki K, Kashima A, Ishitani R, Sugita Y, *Nureki O and *Tsukazaki T. Crystal Structures of SecYEG in Lipidic Cubic Phase Elucidate a Precise Resting and a Peptide-Bound State. Cell Rep. 13, 1561-1568 (2015)
  25. Shimokawa-Chiba N, Kumazaki K, Tsukazaki T, Nureki O, Ito K and Chiba S. Hydrophilic microenvironment required for the channel-independent insertase function of YidC protein. Proc. Natl. Acad. Sci. USA 112, 5063-5068 (2015).
  26. Kumazaki K, Chiba S, Takemoto M, Furukawa A, Nishiyama K, Sugano Y, Mori T, Dohmae N, Hirata K, Nakada-Nakura Y, Maturana AD, Tanaka Y, Mori H, Sugita Y, Arisaka F, Ito K, Ishitani R, *Tsukazaki T and *Nureki O. Structural basis of Sec-independent membrane protein insertion by YidC. Nature 509, 516-520(2014).
  27. Kumazaki K, Kishimoto T, Furukawa A. Mori H, Tanaka Y, Dohmae N, Ishitani R, *Tsukazaki T and *Nureki O. Crystal structure of Escherichia coli YidC, a membrane protein chaperone and insertase. Sci. Rep. 4, 7299 (2014).
  28. Kumazaki K, *Tsukazaki T, Nishizawa T, Tanaka Y, Kato HE, Nakada-Nakura Y, Hirata K, Mori Y, Suga H, Dohmae N, Ishitani R and *Nureki O. Crystallization and preliminary X-ray diffraction analysis of YidC, a membrane-protein chaperone and insertase from Bacillus halodurans. Acta Crystallogr. F  70, 1056-1060 (2014).
  29. Mio K, Tsukazaki T, Mori H, Kawata M, Moriya T, Sasaki Y, Ishitani R, Ito K, *Nureki O and *Sato C. Conformational variation of the translocon enhancing chaperone SecDF. J. Struct. Funct. Genomics 15, 107-115 (2014). 
  30. Tanaka. Y., Hipolito, C.J., Maturana, A.D., Ito, K., Kuroda, T., Higuchi, T., Katoh, T., Kato, H.E., Hattori, M., Kumazaki, K., Tsukazaki, T., Ishitani, R., Suga, H. and Nureki, O. Structural basis for the drug extrusion mechanism by a MATE multidrug transporter. Nature 496, 247-251(2013).
  31. Doki, S., Kato, H.E., Solcan, N., Iwaki, M., Koyama, M., Hattori, M., Iwase, N., Tsukazaki, T., Sugita, Y., Kandori, H., Newstead, S., Ishitani, R. and Nureki, O. Structural basis for dynamic mechanism of proton-coupled symport by the peptide transporter POT. Proc Natl Acad Sci USA 110, 11343-11348 (2013).
  32. Kato, H.E., Zhang, F., Yizhar, O., Ramakrishnan, C., Nishizawa, T., Hirata, K., Ito, J., Aita, Y., Tsukazaki, T., Hayashi, S., Hegemann, P., Maturana, A.D., Ishitani, R., Deisseroth, K. and Nureki O. Crystal structure of the channelrhodopsin light-gated cation channel. Nature 482, 369-374 (2012).
  33. Tsukazaki, T., Mori, H, Echizen, Y., Ishitani, R., Fukai, S., Tanaka, T., Perederina A., Vassylyev, D.G., Kohno, T., Maturana, A.D., Ito, K. and Nureki, O. Structure and function of a membrane component SecDF that enhances protein export. Nature 474, 235-238 (2011).
  34. Tsukazaki, T. and Nureki, O. The mechanism of protein export enhancement by the SecDF membrane component. BIOPHYSICS, 7 129-133 (2011).
  35. Echizen, Y., Tsukazaki, T., Dohmae, N., Ishitani, R. and Nureki, O. Crystallization and preliminary X-ray diffraction of the first periplasmic domain of SecDF, a translocon-associated membrane protein, from Thermus thermophilus.  Acta Crystallogr. F  67, 1367-1370 (2011).
  36. Mori, T., Ishitani, R., Tsukazaki, T., Nureki, O. and Sugita, Y. Molecular mechanisms underlying the early stage of protein translocation through the Sec translocon. Biochemistry 49, 945-950 (2010).
  37. Hattori, M., Iwase, N., Furuya, N., Tanaka, Y., Tsukazaki, T., Ishitani, R., Maguire, M.E., Ito, K., Maturana, A.D.  and Nureki, O. Mg2+-dependent gating of bacterial MgtE channel underlies Mg2+ homeostasis. EMBO J. 28, 3602-3612 (2009)
  38. Tsukazaki, T., Mori, H., Fukai, S., Ishitani, R., Mori, T., Dohmae, N., Perederina, A., Sugita, Y., Vassylyev, D.G., Ito, K. and Nureki, O. Conformational transition of Sec machinery inferred from bacterial SecYE structures. Nature 455, 988-991 (2008).
  39. Tsukazaki, T., Mori, H., Fukai, S., Numata, T., Perederina, A., Adachi, H., Matsumura, H., Takano, K., Murakami, S., Inoue, T., Mori, Y., Sasaki, T., Vassylyev, D.G., Nureki, O. and Ito, K. Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus.  Acta Crystallogr. F  62, 376-380 (2006).
  40. Vassylyev, D.G., Mori, H., Vassylyeva, M.N., Tsukazaki, T., Kimura, Y., Tahirov, T.H. and Ito, K. Crystal structure of the translocation ATPase SecA from Thermus thermophilus reveals a parallel, head-to-head dimer. J. Mol. Biol. 364, 248-258 (2006).
  41. Vassylyeva, M.N., Mori, H., Tsukazaki, T., Yokoyama, S., Tahirov, T.H., Ito, K. and Vassylyev, D.G. Cloning, expression, purification, crystallization and initial crystallographic analysis of the preprotein translocation ATPase SecA from Thermus thermophilus.  Acta Crystallogr. F  62, 909-912 (2006).
  42. Mori, H., Tsukazaki, T., Masui, R., Kuramitsu, S., Yokoyama, S., Johnson, A.E., Kimura, Y., Akiyama, Y. and Ito, K., Fluorescence resonance energy transfer analysis of protein translocase. SecYE from Thermus thermophilus HB8 forms a constitutive oligomer in membranes. J. Biol. Chem. 278, 14257-14264 (2003).
  43. Hirota, S., Tsukazaki, T. and Yamauchi, O. Interactions of cytochrome c peroxidase with lysine peptides. Biochem. Biophys. Res. Commun. 268, 395-397 (2000)
  44. Hirota, S., Endo, M., Hayamizu, K., Tsukazaki, T., Takabe, T., Kohzuma, T. and Yamauchi, O. Interactions of Cytochrome c and Cytochrome f with Aspartic Acid Peptides. J. Am. Chem. Soc. 121, 849-855. (1999)
  45. Hirota, S., Endo, M., Tsukazaki, T., Takabe, T. and Yamauchi, O. Effects of charged peptides on electron transfer from [Fe(CN)6]4- to cytochrome c or plastocyanin. J. Biol. Inor. Chem. 3, 563-569 (1998).

Reviews

  1. 塚崎智也「構造解析からみえてきたタンパク質膜透過駆動モーター膜タンパク質SecDFの仕組み」生化学 92, 717-721 (2020)
  2. 熊崎薫，塚崎智也「膜タンパク質YidCによるタンパク質膜組み込みの構造基盤」膜タンパク質工学ハンドブック 307-315 (2020)
  3. 春山隆充，塚崎智也「高速原子間力顕微鏡によるナノディスクを用いた膜タンパク質のリアルタイム動態観察」野口研究所時報 62, 42-49 (2019) [野口遵研究助成金などによる成果]
  4. 塚崎智也．「タンパク質膜透過装置の構造生物学」(総説) 生物物理 58, 78-82 (2018)
  5. 塚崎智也.　「タンパク質膜透過駆動モーターSecDFの分子機構」医学のあゆみ 262, 367-372 (2017)
  6. 塚崎智也．「タンパク質を膜透過させる分子装置の活写」生化学 88, 114-118 (2016)
  7. Kumazaki, K, Tsukazaki, T. and Nureki, O. 「Crystal structure of YidC reveals a mechanism of Sec-independent membrane protein.」 SPring-8 Research Frontiers 2014, 26-27 (2015)
  8. 塚崎智也．「タンパク質立体構造散歩　タンパク質膜組込み酵素YidC」生物物理 55, 54 (2015)
  9. 塚崎智也．「２つのSecモータータンパク質による蛋白質膜透過のしくみ」実験医学(増刊  構造生命科学で何がわかるのか，何ができるのか 田中啓二，若槻壮市  編), 32, 1571-1575 (2014)
  10. 熊崎 薫，千葉志信，塚崎智也，濡木 理．「膜組み込み酵素YidCによるタンパク質の細胞膜への組み込みの分子機構」新着論文レビュー，http://first.lifesciencedb.jp/archives/8680 (2014)
  11. 塚崎智也，濡木理「タンパク質膜透過装置Secトランスロコン複合体」膜タンパク質構造研究 岩田 想 編, p44-52
  12. 森博幸，塚崎智也．「細菌のタンパク質分泌泌を促進する 膜タンパク質 SecDF の構造と機能」化学と生物，51, 28-35 (2013)
  13. Tsukazaki, T. and Nureki, O. 「Crystal structure of SecDF, a Sec translocon-associated membrane protein.」 SPring-8 Research Frontiers 2011, 22-23 (2012).
  14. 塚崎智也． 「Sec トランスロコンと共に機能するSecDF 膜タンパク質の構造」生物物理 51, 236-237 (2011)
  15. 塚崎智也，森博幸，伊藤維昭，濡木理. 「タンパク質の膜透過を促進する膜タンパク質SecDF の構造と機能」新着論文レビュー, http://first.lifesciencedb.jp/archives/2915 (2011).
  16. 塚崎智也，濡木理. 「タンパク質を膜透過させる分子装置」 化学工業 62, 474-477 (2011)
  17. 塚崎智也. 「Ｘ線結晶構造解析から解明されたSecDF膜タンパク質の構造」東京大学アイソトープセンターニュース, 42(2), 8-13 (2011)
  18. Tsukazaki, T. and Nureki, O. 「Conformational Transition of Sec Machinery Inferred from Bacterial SecYE Structures.」 SPring-8 Research Frontiers 009, 30-31 (2010).
  19. 塚崎智也. 「結晶化用蛋白質の精製法 ~SecDF 膜蛋白質をモデルとして~」　蛋白質科学会アーカイブ 3, e056 (2010).
  20. 塚崎智也, 森博幸. 「細菌型Secトランスロコンの構造から明らかとなったタンパク質膜透過装置の構造変化」生物物理 49, 288-289 (2009)
  21. 森博幸, 塚崎智也. 「立体構造解析からみえてきたSecA による蛋白質の膜透過の駆動機構」蛋白質核酸酵素 54, 685-695 (2009).