Kyushu University Academic Staff Educational and Research Activities Database
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Takashi Nakashima Last modified date:2020.06.12

Assistant Professor / molecular biochemistry
Department of Bioscience and Biotechnology
Faculty of Agriculture

Graduate School
Undergraduate School

 Reseacher Profiling Tool Kyushu University Pure
Academic Degree
Field of Specialization
structural biology
Outline Activities
Structural analysis of the complex of the protein - nucleic acid involved in the translation of the gene
Research Interests
  • Strucutre analysis of archaeal RNA helicase
    keyword : helicase, enzyme, RNA
Academic Activities
1. Makoto Kimura, Kosuke Oshima, Xuzhu Gao, Dan Jiang, Takashi Nakashima, Toshifumi Ueda, Structure and function of archaeal ribonuclease P. In Nucleic Acids and Molecular Biology, Springer,, vol.32, 159-175, 2017.10.
1. 高緒柱,大嶋浩介,上田敏史,中島 崇, 木村 誠, A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3, JOURNAL OF BIOCHEMISTRY, 10.1016/j.bbrc.2017.09.085, 493, 2, 1063-1068, 2017.11.
2. 中島 崇, 木村 誠, Functional characterization of archaeal homologs of human nuclear RNase P proteins Rpp21 and Rpp29 provides insights into the molecular basis of their cooperativity in catalysis, JOURNAL OF BIOCHEMISTRY, 10.1016/j.bbrc.2016.10.142, 482, 1, 68-74, 2017.01.
3. 中島 崇, 木村 誠, Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38, JOURNAL OF BIOCHEMISTRY, 10.1016/j.bbrc.2016.04.118, 474, 3, 541-546, 2016.06.
4. Takashi Nakashima, Yoshimitsu Kakuta, makoto kimura, Ueda T, Suematsu K, On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis., Biosci Biotechnol Biochem. , 23, 1-8, 2015.02.
5. Takashi Nakashima, makoto kimura, Yoshimitsu Kakuta, Imai T, Ueda T, Hazeyama K, Furutani T, Enhancement of RNA annealing and strand displacement found in archaeal ribonuclease P proteins is conserved in Escherichia coli protein C5 and yeast protein Rpr2., Biosci Biotechnol Biochem. , 78, 10, 1700-1702, 2014.10.
6. Takashi Nakashima, Yoshimitsu Kakuta, makoto kimura, Takahiro Nakamura, Imai T, Maeda T, Pentatricopeptide repeat motifs in the processing enzyme PRORP1 in Arabidopsis thaliana play a crucial role in recognition of nucleotide bases at TψC loop in precursor tRNAs., Biochem Biophys Res Commun. , 450, 4, 1541-1546, 2014.08.
7. Toshihumi Ueda, Hiroshi Yamaguchi, Mitsuru Miyanoshita, Takashi Nakashima, Yoshimitsu Kakuta, makoto kimura, Characterization of the peripheral structures of archaeal RNase P RNA from Pyrococcus horikoshii OT3.
, J Biochem. , 155, 1, 25-33, 2014.01.
8. Takashi Nakashima, makoto kimura, Yoshimitsu Kakuta, Characterization of the peripheral structures of archaeal RNase P RNA from Pyrococcus horikoshii OT3., J Biochem, 2014.01.
9. Takashi Nakashima, M. IshiHara, T. Ueda, Etsuko Nishimoto, Yoshimitsu Kakuta, makoto kimura, Extra-structural elements in the RNA recognition motif in archaeal Pop5 play a crucial role in the activation of RNase P RNA from Pyrococcus horikoshii OT3.

, Biochem Biophys Res Commun. , 440, 4, 594-598, 2013.11.
10. Zwieb C, Nakao Y, Nakashima T, Takagi H, Goda S, Andersen ES, Kakuta Y, Kimura M., Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3., Biochem Biophys Res Commun., 414, 3, 517-522, 2011.10, Ribonuclease P (RNase P) is a ubiquitous trans-acting ribozyme that processes the 5' leader sequence of precursor tRNA (pre-tRNA). The RNase P RNA (PhopRNA) of the hyperthermophilic archaeon Pyrococcus horikoshii OT3 is central to the catalytic process and binds five proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38) which contribute to the enzymatic activity of the holoenzyme. Despite significant progress in determining the crystal structure of the proteins, the structure of PhopRNA remains elusive. Comparative analysis of the RNase P RNA sequences and existing crystallographic structural information of the bacterial RNase P RNAs were combined to generate a phylogenetically supported three-dimensional (3-D) model of the PhopRNA. The model structure shows an essentially flat disk with 16 tightly packed helices and a conserved face suitable for the binding of pre-tRNA. Moreover, the structure in solution was investigated by enzymatic probing and small-angle X-ray scattering (SAXS) analysis. The low resolution model derived from SAXS and the comparative 3-D model have similar overall shapes. The 3-D model provides a framework for a better understanding of structure-function relationships of this multifaceted primordial ribozyme..
11. Hara T, Terada A, Yamaguchi H, Nakashima T, Kakuta Y, Kimura M., The contribution of peripheral stem-loops to the catalytic activity of archaeal RNase P RNA from Pyrococcus horikoshii OT3., Biosci Biotechnol Biochem. , 75, 4, 816-819, 2011.04.
12. M.Shinohara, J.X. Guo, M. Mori, T. Nakashima, H. Takagi, E. Nishimoto, S. Yamashita, K. Tsumoto, Y. Kakuta, and M. Kimura, The sturctural mechanism of the inhibition of archaeal RelE toxin by iots cognate RelB antitoxin., Biochem. Biophys. Res. Commun., 2010.09.
13. Kosaka S, Hada K, Nakashima T, Kimura M. , Structural changes in ribonuclease P RNA in the hyperthermophilic archaeon Pyrococcus horikoshii OT3 induced on interaction with proteins., Biosci Biotechnol Biochem., 74(2):394-396., 2010.02.
14. Kikutake C, Shinohara M, Takagi H, Nakashima T, Kimura M., The C-terminal portion of an archaeal toxin, aRelE, plays a crucial role in protein synthesis inhibition., Biosci Biotechnol Biochem. , 73(12):2766-2778., 2009.12.
15. Zhang X, Nakashima T, Kakuta Y, Yao M, Tanaka I, Kimura M. , Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3.
, Protein Science, 17(1),136-45. (2008)
, 2008.01.
16. Shin Kawano, Takashi Nakashima, Yoshimitsu Kakuta, Isao Tanaka, Makoto Kimura , Crystal structure of protein Ph1481p in complex with protein Ph1877p of archaeal RNase P from Pyrococcus horikoshii OT3: implication of dimer formation of the holoenzyme, Journal of Moleculer Biology, 357(2),583-591, 2006.01.
17. T. Nakashima, M. Kimura, A. Nakagawa and I. Tanaka, Crystallization and preliminary X-ray crystallographic study of a 23S rRNA binding domain of the ribosomal protein L2 from Bacillus stearothermophilus, Journal of Structural Biology, 10.1006/jsbi.1998.4053, 124, 1, 99-101, 124, 99-101, 1998.12.
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Educational Activities
Other Educational Activities
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Professional and Outreach Activities