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Research Output 1998 2018

  • 476 Citations
  • 12 h-Index
  • 38 Article
2018
3 Citations (Scopus)

Crystal structures of the archaeal RNase P protein Rpp38 in complex with RNA fragments containing a K-turn motif

Oshima, K., Gao, X., Hayashi, S., Ueda, T., Nakashima, T. & Kimura, M., Jan 2018, In : Acta Crystallographica Section F: Structural Biology Communications. 74, 1, p. 57-64 8 p.

Research output: Contribution to journalArticle

Ribonuclease P
Crystal structure
fragments
RNA
proteins
2017
3 Citations (Scopus)

A three-dimensional model of RNase P in the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Gao, X., Oshima, K., Ueda, T., Nakashima, T. & Kimura, M., Nov 18 2017, In : Biochemical and Biophysical Research Communications. 493, 2, p. 1063-1068 6 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
Archaea
RNA
Proteins
2 Citations (Scopus)
Ribonuclease P
Catalysis
Proteins
Pyrococcus horikoshii
Chemical activation
1 Citation (Scopus)

Variations in the expression of photosynthesis-related proteins in field Chattonella marina cells during a harmful algal bloom

Qiu, X., Mukai, K., Shimasaki, Y., Tsuyama, M., Matsubara, T., Nakashima, T., Ichinose, H., Nakajima, Y., Honjo, I. & Oshima, Y., Sep 1 2017, In : Journal of the Faculty of Agriculture, Kyushu University. 62, 2, p. 373-380 8 p.

Research output: Contribution to journalArticle

Harmful Algal Bloom
Photosynthesis
algal blooms
photosynthesis
physiological response
2016
4 Citations (Scopus)

Functional implication of archaeal homologues of human RNase P protein pair Pop5 and Rpp30

Hamasaki, M., Hazeyama, K., Iwasaki, F., Ueda, T., Nakashima, T., Kakuta, Y. & Kimura, M., Jan 1 2016, In : Journal of biochemistry. 159, 1, p. 31-40 10 p.

Research output: Contribution to journalArticle

Ribonuclease P
Surface Plasmon Resonance
Surface plasmon resonance
Pyrococcus horikoshii
Chemical activation
8 Citations (Scopus)

Structural basis for recognition of a kink-turn motif by an archaeal homologue of human RNase P protein Rpp38

Oshima, K., Kakiuchi, Y., Tanaka, Y., Ueda, T., Nakashima, T., Kimura, M. & Yao, M., Jun 3 2016, In : Biochemical and Biophysical Research Communications. 474, 3, p. 541-546 6 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
RNA
Proteins
Ribosomal Proteins
2015
1 Citation (Scopus)
Ribonuclease P
Nucleic Acid Hybridization
Nucleic Acids
DNA
Fluorescence Resonance Energy Transfer
1 Citation (Scopus)
Thermococcus
Ribonuclease P
Gene encoding
Archaea
RNA Precursors
3 Citations (Scopus)

On archaeal homologs of the human RNase P proteins Pop5 and Rpp30 in the hyperthermophilic archaeon Thermococcus kodakarensis

Suematsu, K., Ueda, T., Nakashima, T., Kakuta, Y. & Kimura, M., Jan 1 2015, In : Bioscience, Biotechnology and Biochemistry. 79, 6, p. 952-959 8 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Thermococcus
Ribonuclease P
Archaea
RNA Precursors
2014
3 Citations (Scopus)

Characterization of putative toxin/antitoxin systems in Vibrio parahaemolyticus

Hino, M., Zhang, J., Takagi, H., Miyoshi, T., Uchiumi, T., Nakashima, T., Kakuta, Y. & Kimura, M., Jan 1 2014, In : Journal of Applied Microbiology. 117, 1, p. 185-195 11 p.

Research output: Contribution to journalArticle

Vibrio parahaemolyticus
Antitoxins
Escherichia coli
Multigene Family
Growth
6 Citations (Scopus)

Characterization of the peripheral structures of archaeal RNase P RNA from Pyrococcus horikoshii OT3

Ueda, T., Yamaguchi, H., Miyanoshita, M., Nakashima, T., Kakuta, Y. & Kimura, M., Jan 27 2014, In : Journal of Biochemistry. 155, 1, p. 25-33 9 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
RNA
RNA Precursors
Proteins

Enhancement of RNA annealing and strand displacement found in archaeal ribonuclease P proteins is conserved in Escherichia coli protein C5 and yeast protein Rpr2

Furutani, T., Hazeyama, K., Ueda, T., Tomita, S., Imai, T., Nakashima, T., Kakuta, Y. & Kimura, M., Jan 1 2014, In : Bioscience, Biotechnology and Biochemistry. 78, 10, p. 1700-1702 3 p.

Research output: Contribution to journalArticle

Ribonuclease P
Fungal Proteins
Escherichia coli Proteins
RNA
Annealing
14 Citations (Scopus)
RNA Precursors
Arabidopsis
Nucleotides
Ribonuclease P
RNA, Transfer, Phe
2013
6 Citations (Scopus)
Pyrococcus horikoshii
Ribonuclease P
Fluorescence Resonance Energy Transfer
Chemical activation
RNA Precursors
5 Citations (Scopus)

Growth-phase dependent variation in photosynthetic activity and cellular protein expression profile in the harmful raphidophyte Chattonella antiqua

Qiu, X., Shimasaki, Y., Tsuyama, M., Yamada, T., Kuwahara, R., Kawaguchi, M., Honda, M., Gunjikake, H., Tasmin, R., Shimizu, M., Sato, Y., Kato-Unoki, Y., Nakashima, T., Matsubara, T., Yamasaki, Y., Ichinose, H., Wariishi, H., Honjo, T. & Oshima, Y., Feb 14 2013, In : Bioscience, Biotechnology and Biochemistry. 77, 1, p. 46-52 7 p.

Research output: Contribution to journalArticle

Cell growth
Growth
Proteins
Peroxiredoxins
Photosystem II Protein Complex
2 Citations (Scopus)

Thiobencarb herbicide reduces growth, photosynthetic activity, and amount of rieske iron-sulfur protein in the diatom Thalassiosira pseudonana

Shimasaki, Y., Tsuyama, M., Tasmin, R., Qiu, X., Shimizu, M., Sato, Y., Yamasaki, Y., Kato-Unoki, Y., Nukata, A., Nakashima, T., Ichinose, H., Wariishi, H., Honjo, T. & Oshima, Y., Sep 1 2013, In : Journal of Biochemical and Molecular Toxicology. 27, 9, p. 437-444 8 p.

Research output: Contribution to journalArticle

Diatoms
Herbicides
Growth
Electron Transport
Proteins
2012
5 Citations (Scopus)

Thermodynamic analysis of a multifunctional RNA-binding protein, PhoRpp38, in the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Oshima, K., Nakashima, T., Kakuta, Y., Tsumoto, K. & Kimura, M., Jun 29 2012, In : Bioscience, Biotechnology and Biochemistry. 76, 6, p. 1252-1255 4 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
RNA-Binding Proteins
Archaea
Thermodynamics
2011
9 Citations (Scopus)

Crystallographic survey of active sites of an unclassified glutathione transferase from Bombyx mori

Kakuta, Y., Usuda, K., Nakashima, T., Kimura, M., Aso, Y. & Yamamoto, K., Dec 1 2011, In : Biochimica et Biophysica Acta - General Subjects. 1810, 12, p. 1355-1360 6 p.

Research output: Contribution to journalArticle

Bombyx
Insecticides
Glutathione Transferase
Catalytic Domain
Glutathione
27 Citations (Scopus)

Crystal structure of the branching enzyme i (BEI) from Oryza sativa L with implications for catalysis and substrate binding

Noguchi, J., Chaen, K., Vu, N. T., Akasaka, T., Shimada, H., Nakashima, T., Nishi, A., Satoh, H., Omori, T., Kakuta, Y. & Kimura, M., Aug 1 2011, In : Glycobiology. 21, 8, p. 1108-1116 9 p.

Research output: Contribution to journalArticle

1,4-alpha-Glucan Branching Enzyme
Catalysis
Crystal structure
Substrates
Amylases
12 Citations (Scopus)

Immunological characterization of honey proteins and identification of MRJP 1 as an IgE-binding protein

Hayashi, T., Takamatsu, N., Nakashima, T. & Arita, T., Apr 13 2011, In : Bioscience, Biotechnology and Biochemistry. 75, 3, p. 556-560 5 p.

Research output: Contribution to journalArticle

Galectin 3
Honey
Immunoglobulin E
Proteins
Taraxacum
23 Citations (Scopus)
Bombyx
Insecticides
Glutathione Transferase
Amino Acids
Enzymes
11 Citations (Scopus)

Structural modeling of RNase P RNA of the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Zwieb, C., Nakao, Y., Nakashima, T., Takagi, H., Goda, S., Andersen, E. S., Kakuta, Y. & Kimura, M., Oct 28 2011, In : Biochemical and Biophysical Research Communications. 414, 3, p. 517-522 6 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
Archaea
RNA
Catalytic RNA
4 Citations (Scopus)

The contribution of peripheral stem-loops to the catalytic activity of archaeal RNase P RNa from Pyrococcus horikoshii OT3

Hara, T., Terada, A., Yamaguchi, H., Nakashima, T., Kakuta, Y. & Kimura, M., May 16 2011, In : Bioscience, Biotechnology and Biochemistry. 75, 4, p. 816-819 4 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
Catalyst activity
RNA Precursors
Catalysis
2010
4 Citations (Scopus)

Structural changes in ribonuclease P RNA in the hyperthermophilic archaeon pyrococcus horikoshii OT3 induced on interaction with proteins

Kosaka, S., Hada, K., Nakashima, T. & Kimura, M., Mar 1 2010, In : Bioscience, Biotechnology and Biochemistry. 74, 2, p. 394-396 3 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Ribonuclease P
Archaea
RNA
Circular Dichroism
6 Citations (Scopus)

The structural mechanism of the inhibition of archaeal RelE toxin by its cognate RelB antitoxin

Shinohara, M., Guo, J. X., Mori, M., Nakashima, T., Takagi, H., Nishimoto, E., Yamashita, S., Tsumoto, K., Kakuta, Y. & Kimura, M., Sep 1 2010, In : Biochemical and Biophysical Research Communications. 400, 3, p. 346-351 6 p.

Research output: Contribution to journalArticle

Antitoxins
Escherichia coli
Pyrococcus horikoshii
Archaea
Titration
2009
48 Citations (Scopus)

Molecular and biochemical characterization of a Zeta-class glutathione S-transferase of the silkmoth

Yamamoto, K., Shigeoka, Y., Aso, Y., Banno, Y., Kimura, M. & Nakashima, T., May 1 2009, In : Pesticide Biochemistry and Physiology. 94, 1, p. 30-35 6 p.

Research output: Contribution to journalArticle

Bombyx
permethrin
Glutathione Transferase
Permethrin
glutathione transferase
1 Citation (Scopus)

The C-terminal portion of an archaeal toxin, aRelE, plays a crucial role in protein synthesis inhibition

Kikutake, C., Shinohara, M., Takagi, H., Nakashima, T. & Kimura, M., Dec 1 2009, In : Bioscience, Biotechnology and Biochemistry. 73, 12, p. 2766-2768 3 p.

Research output: Contribution to journalArticle

Ribosomes
Pyrococcus horikoshii
Carrier Proteins
Proteins
Amino Acids
2008
16 Citations (Scopus)

Biochemical and crystallographic characterization of the starch branching enzyme I (BEI) from Oryza sativa L

Vu, N. T., Shimada, H., Kakuta, Y., Nakashima, T., Ida, H., Omori, T., Nishi, A., Satoh, H. & Kimura, M., Dec 1 2008, In : Bioscience, Biotechnology and Biochemistry. 72, 11, p. 2858-2866 9 p.

Research output: Contribution to journalArticle

1,4-alpha-Glucan Branching Enzyme
Amylopectin
Amylases
Enzymes
Amylose
16 Citations (Scopus)

Crystal structure and functional analysis of an archaeal chromatin protein alba from the hyperthermophilic archaeon Pyrococcus horikoshii OT3

Hada, K., Nakashima, T., Osawa, T., Shimada, H., Kakuta, Y. & Kimura, M., Apr 7 2008, In : Bioscience, Biotechnology and Biochemistry. 72, 3, p. 749-758 10 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
Archaeal Proteins
Functional analysis
Archaea
Ribonuclease P
6 Citations (Scopus)

Crystal structure of an archaeal Ski2p-like protein from Pyrococcus horikoshii OT3

Zhang, X., Nakashima, T., Kakuta, Y., Yao, M., Tanaka, I. & Kimura, M., Jan 1 2008, In : Protein Science. 17, 1, p. 136-145 10 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
RNA Helicases
Archaea
RNA Stability
Escherichia coli
2006
54 Citations (Scopus)
Pyrococcus horikoshii
Archaeal Proteins
Ribonuclease P
Holoenzymes
Protein Subunits
5 Citations (Scopus)

Crystal structures of the Nicotiana glutinosa ribonuclease NT in complex with nucleoside monophosphates

Kawano, S., Kakuta, Y., Nakashima, T. & Kimura, M., Sep 1 2006, In : Journal of biochemistry. 140, 3, p. 375-381 7 p.

Research output: Contribution to journalArticle

Ribonucleases
Nucleosides
Tobacco
Crystal structure
Guanosine Monophosphate
25 Citations (Scopus)

In vitro reconstitution of the GTPase-associated centre of the archaebacterial ribosome: The functional features observed in a hybrid form with Escherichia coli 50S subunits

Nomura, T., Nakano, K., Maki, Y., Naganuma, T., Nakashima, T., Tanaka, I., Kimura, M., Hachimori, A. & Uchiumi, T., Jun 15 2006, In : Biochemical Journal. 396, 3, p. 565-571 7 p.

Research output: Contribution to journalArticle

Pyrococcus horikoshii
GTP Phosphohydrolases
Ribosomes
Escherichia coli
L 012
2005
42 Citations (Scopus)

Molecular basis of alanine discrimination in editing site

Sokabe, M., Okada, A., Yao, M., Nakashima, T. & Tanaka, I., Aug 16 2005, In : Proceedings of the National Academy of Sciences of the United States of America. 102, 33, p. 11669-11674 6 p.

Research output: Contribution to journalArticle

Alanine-tRNA Ligase
RNA, Transfer, Ala
Alanine
Serine
Zinc
2001
17 Citations (Scopus)

Ribosomal protein L5 has a highly twisted concave surface and flexible arms responsible for rRNA binding

Nakashima, T., Yao, M., Kawamura, S., Iwasaki, K., Kimura, M. & Tanaka, I., May 16 2001, In : RNA. 7, 5, p. 692-701 10 p.

Research output: Contribution to journalArticle

Haloarcula marismortui
Geobacillus stearothermophilus
Amino Acids
Mutation
Static Electricity
1999
29 Citations (Scopus)

Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 Å resolution

Nakagawa, A., Tanaka, I., Sakai, R., Nakashima, T., Funatsu, G. & Kimura, M., Aug 17 1999, In : Biochimica et Biophysica Acta - Protein Structure and Molecular Enzymology. 1433, 1-2, p. 253-260 8 p.

Research output: Contribution to journalArticle

Momordica charantia
Ribonucleases
Seed
Seeds
Crystal structure
49 Citations (Scopus)

The three-dimensional structure of the RNA-binding domain of ribosomal protein L2; a protein at the peptidyl transferase center of the ribosome

Nakagawa, A., Nakashima, T., Taniguchi, M., Hosaka, H., Kimura, M. & Tanaka, I., Mar 15 1999, In : EMBO Journal. 18, 6, p. 1459-1467 9 p.

Research output: Contribution to journalArticle

Peptidyl Transferases
Ribosomes
RNA
Geobacillus stearothermophilus
X ray crystallography
1998
5 Citations (Scopus)

Crystallization and preliminary X-ray crystallographic study of a 23S rRNA binding domain of the ribosomal protein L2 from Bacillus stearothermophilus

Nakashima, T., Kimura, M., Nakagawa, A. & Tanaka, I., Dec 1 1998, In : Journal of structural biology. 124, 1, p. 99-101 3 p.

Research output: Contribution to journalArticle

Geobacillus stearothermophilus
Crystallization
Large Ribosome Subunits
X-Rays
Synchrotrons