[Kyoto Univ.] [Grad. Sch. Sci.] [Dept. Chem.] [Biol. Struct. Chem.] [Miki Group] [Members]
Japanese
Last updated on 2013/06/01

NAKAMURA's HOMEPAGE

Our recent article was introduced in the website of RIKEN RESEARCH (2008/03/21).
Our recent article was introduced in the website of Kyoto University (2007/11/13).
Our recent article was introduced in the website of SPring-8 (2007/11/13).

Publications Presentations (Academic Society) Presentations (Others) Academic Society Affiliations Links
Name: Akira NAKAMURA
Birthplace: Katsuyama, Fukui, Japan
Hometown: Tokai, Aichi, Japan
Birthday December 3rd, 1978
Birthflower: Lavender, Quince, Chrysanthemum
Birthstone Turquoise (triclinic system; CuAl6(PO4)4(OH)8 4H2O)
Ruby (hexagonal system; Al2O3+Cr)
White Jade (monoclinic system; NaAlSi2O6)
Lapis lazuli (mixture of several different minerals including lazurite, sodalite, and so on)
Tanzanite (orthorhombic system; Ca2Al3(SiO4)3(OH))
Academic background
March, 1997 Graduated from Yokosuka High School (Aichi, Japan)
Apr., 1997 - Mar., 2001 Faculty of Science, Kyoto University (Kyoto, Japan)
March 26, 2001 Bachelor of Science, Kyoto University (Division of Chemistry)
Apr., 2001 - Mar., 2003 Department of Chemistry, Graduate School of Science, Kyoto University
March 24, 2003 Master of Science, Kyoto University
Apr., 2003 - Mar., 2006 Department of Chemistry, Graduate School of Science, Kyoto University
March 23, 2007 Ph.D. in Science, Kyoto University
Dissertation Structural studies on replication initiator protein RepE of F plasmid
Career
Sep., 2002 - Nov., 2002 Teaching Assistant (Chemical Experiment C; Division of Chemistry, Faculty of Science)
Sep., 2003 - Nov., 2003 Teaching Assistant (Chemical Experiment C; Division of Chemistry, Faculty of Science)
Jun., 2004 - Mar., 2004 Research Assistant (Kyoto University Alliance for Chemistry, 21st Century COE Program)
Jun., 2004 - Oct., 2004 Teaching Assistant (Chemical Experiment C; Division of Chemistry, Faculty of Science)
Jul., 2004 - Mar., 2005 Research Assistant (Kyoto University Alliance for Chemistry, 21st Century COE Program)
Jun., 2005 - Dec., 2005 Research Assistant (Kyoto University Alliance for Chemistry, 21st Century COE Program)
Apr., 2006 - Mar., 2007 Postdoctral Fellow (Graduate School of Science, Kyoto University;
National Project on Protein Structural and Functional Analyses)
Apr., 2007 - Mar., 2008 Postdoctral Fellow (Graduate School of Science, Kyoto University, Scientific Research)
Apr., 2008 - Mar., 2009 Postdoctral Fellow (Graduate School of Science, Kyoto University;
Targeted Proteins Research Program)
April, 2009 - Mar., 2010 Postdoctral Fellow (Graduate School of Science, Kyoto University;
Targeted Proteins Research Program)
April, 2010 - The University of Tokyo Graduate School of Agricultural and Life Sciences Project Research Associate(JST Development of Systems and Technology for Advanced Measurement and Analysis
Research Field
Protein Crystallography, Structural Biology
Topics of Research
  • Structure and function of DNA-binding protein
  • Structure and function of Molecular Chaperone
  • Structure and function of Enzymes related to the novel carbon fixation in Archaea
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Publications

  1. Nakamura, A., Komori, H., Kobayashi, G., Kita, A., Wada, C. and Miki, K.
    The N-terminal domain of the replication initiator protein RepE is a dimerization domain forming a stable dimer.
    Biochemical and Biophysical Research Communications
    27 February 2004; Volume 315, Issue 1, Pages 10-15
    (PUBMED)

  2. Fujihashi, M., Numoto, N., Kobayashi, Y., Mizushima, A., Tsujimura, M., Nakamura, A., Kawarabayashi, Y. and Miki, K.
    Crystal Structure of Archaeal Photolyase from Sulfolobus tokodaii with Two FAD Molecules: Implication of a Novel Light-harvesting Cofactor.
    Journal of Molecular Biology
    26 January 2007; Volume 365, Issue 4, Pages 903-910
    (PUBMED) (PDB:2E0I)

  3. Nakamura, A., Sosa, A., Komori, H., Kita, A. and Miki, K.
    Crystal structure of TTHA1657 (AT-rich DNA-binding protein; p25) from Thermus thermophilus HB8 at 2.16 A resolution.
    Proteins: Structure, Function, and Bioinformatics
    15 February 2007; Volume 66, Issue 3, Pages 755-759
    (PUBMED) (PDB:2DT5)

  4. Nakamura, A., Wada, C. and Miki, K.
    Expression and purification of F-plasmid RepE and preliminary X-ray crystallographic study of its complex with operator DNA.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications
    1 April 2007; Volume 63, Part 4, Pages 346-349
    (PUBMED)

  5. Nakamura, A., Wada, C. and Miki, K.
    Structural basis for regulation of bifuctional roles in replication initiator protein.
    Proceedings of the National Academy of Science of the United States of America
    20 November 2007; Volume 104, Issue 47, Pages 18484-18489
    (PUBMED) (PDB:2Z9O)

  6. Nakamura, A., Takumi, K., and Miki, K.
    Crystal structure of a thermophilic GrpE protein: Insight into thermosensing function for the DnaK chaperone system.
    Journal of Molecular Biology
    05 March 2010; Volumes 396, Issue 4,Pages 1000-1011
    (PUBMED) (PDB:3A6M)

  7. Nakamura, A.,* Ohtsuka, J.,* Miyazono, K.,* Yamamura, A., Kubota, K., Hirose, R., Hirota, N., Ataka, M., Sawano, Y., and Tanokura, M. (* Equal contribution)
    Improvement in quality of protein crystals grown in a high magnetic field gradient.
    Crystal Growth & Design
    27 February 2012; Volume 12, Issue 3, Pages 1141-1150

  8. Nakamura, A., Fujihashi, M., Aono, R., Sato, T., Nishiba, Y., Yoshida, S., Yano, A., Atomi, H., Imanaka, T., and Miki, K.
    Dynamic, ligand-dependent conformational change triggers reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis KOD1.
    The Journal of Biological Chemistry
    15 June 2012; Volume 287, Issue 25, Pages 20784-20796
    (PUBMED) (PDB:3A11, 3A9C, 3VM6)

  9. Okai, M., Ohtsuka, J., Asano, A., Guo, L., Miyakawa, T., Miyazono, K., Nakamura, A., Okada, A., Zheng, H., Kimura, K., Nagata, K., and Tanokura, M.
    High pressure refolding, purification, and crystallization of flavin reductase from Sulfolobus tokodaii strain 7.
    Protein Expression and Purification
    August 2012; Volume 84, Issue 2, Pages 214-218
    (PUBMED)

  10. Qin, H.-M., Miyakawa, T., Nakamura, A., Xue, Y.-L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, J., and Tanokura, M.
    Expression, purification, crystallization and preliminary X-ray analysis of a novel N-substituted branched-chain L-amino-acid dioxygenase from Burkholderia ambifaria AMMD.
    Acta Crystallographica Section F Structural Biology and Crystallization Communications
    September 2012; Volume 68, Part 9, Pages 1067-1069
    (PUBMED)

  11. Nishitani, Y., Aono, R., Nakamura, A., Sato, T., Atomi, H., Imanaka, T., and Miki K.
    Structure analysis of archaeal AMP phosphorylase reveals two unique modes of dimerization.
    Journal of Molecular Biology
    07 May 2013 online
    (PUBMED) (PDB:4GA4, 4GA5, 4GA6)

  12. Qin, H.-M., Miyakawa, T., Jia, M.-Z., Nakamura, A., Ohtsuka, J., Xue, Y.-L., Kawashima, T., Kasahara, T., Hibi, M., Ogawa, J., and Tanokura, M.
    Crystal Structure of a Novel N-Substituted L-Amino Acid Dioxygenase from Burkholderia ambifaria AMMD.
    PLoS One
    May 28 2013; Volume 8, Issue 5, Pages e63996
    (PUBMED) (PDB:3W20, 3W21)

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Reviews and Books

  1. Nakamura, A. and Miki, K.
    Regulatory Mechanism of the Initiation of Plasmid DNA Replication (in Japanese)
    Kagaku to Seibutsu
    01 June 2008; Volume 46, Issue 6, Pages 380-385

  2. Nakamura, A. and Miki. K.
    Conformational Changes upon Activation of a Replication Initiator Protein, RepE
    SPring-8 Research Frontiers 2008
    July 2009; Pages 38-39

  3. Akira Nakamura and Masaru Tanokura
    Development of a High-quality Protein Crystal Fromation System with Strong Magnetic Fields of a Superconducting Manget (in Japanese)
    Superconductivity and High Temperature Superconductors
    22 March 2013; Part 2, Chapter 7, Section 2
    NTS, Inc., Tokyo

  4. Okada, H., Hirota, N., Matsumoto, S., Wada, H., Kiyohara, M., Ode, T., Tanokura, M., Nakamura, A. and Ohtsuka, J.
    Development of a protein crystal formation system with a superconducting magnet
    IEEE Transactions on Applied Superconductivity
    June 2013; Volume 23, Issue 3, Page 3700104

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Presentations at Meeting of Academic Society

  1. Akira Nakamura, Hirofumi Komori, Gengo Kobayashi, Chieko Wada, Kunio Miki
    Dimer structure of initiator protein RepE from mini-F plasmid in Escherichia coli.
    The Japanese Biochemical Society The 74th Annual Meeting (Poster) October 25-28(27), 2001
    Kyoto International Conference Hall, Kyoto Takaragaike Prince Hotel, Kyoto, Japan.

  2. Akira Nakamura, Hirofumi Komori, Gengo Kobayashi, Akiko Kita, Chieko Wada, Kunio Miki
    Crystallization of replication initiator protein RepE N-terminal domain dimer.
    Protein Science Society of Japan The 3rd Annual Meeting (Poster) June 23-25(25), 2003
    Sapporo Convention Center, Hokkaido, Japan.

  3. Akira Sosa, Akira Nakamura, Hirofumi Komori, Akiko Kita, Kunio Miki
    Crystal structure of the NAD(H) dependent redox sensing repressor p25 from Thermus thermophilus HB8.
    The Biophysical Society of Japan The 43rd Annual Meeting (Poster) November 23-25(24), 2005
    Sapporo Convention Center, Hokkaido, Japan.

  4. Kouhei Takumi, Akira Nakamura, Kunio Miki
    Crystallographic study of GrpE from Thermus thermophilus HB8.
    Protein Science Society of Japan The 6th Annual Meeting (Poster) April 24-26(26), 2006
    Kyoto International Conference Hall, Kyoto, Japan.

  5. Masahiro Fujihashi, Nobutaka Numoto, Yukiko Kobayashi, Akira Mizushima, Masanari Tsujimura, Akira Nakamura, Yutaka Kawarabayashi, Kunio Miki
    Crystal structure of archaeal hyperthermophilic Photolyase from Sulfolobus tokodaii.
    Protein Science Society of Japan The 6th Annual Meeting (Poster) April 24-26(26), 2006
    Kyoto International Conference Hall, Kyoto, Japan.

  6. Masahiro Fujihashi, Nobutaka Numoto, Yukiko Kobayashi, Akira Mizushima, Masanari Tsujimura, Akira Nakamura, Yutaka Kawarabayashi, Kunio Miki
    Crystal structure of archaeal photolyase with two FAD molecules.
    Asian Crystallographic Association/The Crystallographic Society of Japan AsCA'06/CrSJ (Poster) November 20-23(21), 2006
    Tsukuba International Congress Center Epochal Tsukuba, Ibaraki, Japan.

  7. Akira Nakamura, Chieko Wada, Kunio Miki
    Crystal structure of the F plasmid replication initiator RepE.
    Protein Science Society of Japan The 7th Annual Meeting (Poster) May 24-26(24), 2007
    Sendai International Center, Miyagi, Japan.

  8. Akira Nakamura, Chieko Wada, Kunio Miki
    Conformational Change in Bifunctional Replication Initiator Protein RepE
    Asian Crystallographic Association The 8th Conference (AsCA 2007) (Oral) November 04-07(05), 2007
    Howard International House, Taipei, Taiwan.

  9. Akira Nakamura, Chieko Wada, Kunio Miki
    Conformational changes of the F plasmid replication initiator protein RepE
    The Molecular Biology Society of Japan The 30th Annual Meeting,
    The Japanese Biochemical Society The 80th Annual Meeting
    BMB2007 (Poster/Oral) December 11-15(11/14), 2007
    Pacifico Yokohama, InterContinental YOKOHAMA THE GRAND, Kanagawa, Japan.

  10. Akira Nakamura, Kouhei Takumi, Kunio Miki
    Crystal structure of a co-chaperone GrpE of the DnaK system from Thermus thermophilus HB8.
    Protein Science Society of Japan The 8th Annual Meeting (Poster) June 10-12(11), 2008
    Tower Hall Funabori, Tokyo, Japan.

  11. Akira Nakamura, Chieko Wada, Kunio Miki
    Structural basis for regulation of bifunctional roles of the F-plasmid replication initiator RepE
    Acta Crystallographica Section A Fundations of Crystallography
    August 2008; Volume 64 Supplement, Page C304
    International Union of Crystallography XXI Congress and General Assembly (IUCr 2008) (Poster) August 23-31(24,25), 2008
    GRAND CUBE OSAKA (Osaka International Convention Center), Osaka, Japan.

  12. Akira Nakamura, Masahiro Fujihashi, Yosuke Nishiba, Shosuke Yoshida, Ayumu Yano, Haruyuki Atomi, Tadayuki Imanaka, Kunio Miki
    Crystal structure of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1
    Protein Science Society of Japan The 9th Annual Meeting (Poster) May 20-22(21), 2009
    ANA HOTEL KUMAMOTO NEW SKY, Kumamoto, Japan.

  13. Akira Nakamura, Masahiro Fujihashi, Riku Aono, Takaaki Sato, Yosuke Nishiba, Shosuke Yoshida, Ayumu Yano, Haruyuki Atomi, Tadayuki Imanaka, Kunio Miki
    Crystal structures and reaction mechanism of ribose-1,5-bisphosphate isomerase from Thermococcus kodakaraensis KOD1
    Protein Science Society of Japan The 10th Annual Meeting (Poster) June 16-18(18), 2010
    Sapporo Convention Center, Hokkaido, Japan.

  14. Akira Nakamura, Jun Ohtsuka, Ken-ichi Miyazono, Akihiro Yamamura, Keiko Kubota, Ryoichi Hirose, Noriyuki Hirota, Hitoshi Wada, Mitsuo Ataka, Tatsuki Kashiwagi, Eiichiro Suzuki, Yoriko Sawano, Masaru Tanokura
    Quality Improvement of Protein Crystals under Reduced Gravity Conditions using a Superconducting Magnet
    The Magneto-Science Society of Japan The 6th Annual Meeting (Oral) September 26-28(27), 2011
    Sanjo Conference Hall, The University of Tokyo, Tokyo, Japan.

  15. Tatsuki Kashiwagi, et al., Eiichiro Suzuki, Masaru Tanokura, Akira Nakamura, Jun Ohtsuka, Yoriko Sawano, Motosuke Kiyohara, Takahiro Ode, Akiko Kita, Noriyuki Hirota, Hitoshi Wada
    Development of High-performance and High-quality Protein Crystal Formation System using a Superconducting Magnet and Its Application to Enzymes for Industry
    The Crystallographic Society of Japan Annual Meeting 2011 (Poster) November 24-25, 2011
    Conference Hall (Gakujutsu-koryukaikan), Hokkaido University, Hokkaido, Japan.

  16. Akira Nakamura, Jun Ohtsuka, Ken-ichi Miyazono, Akihiro Yamamura, Keiko Kubota, Ryoichi Hirose, Noriyuki Hirota, Mitsuo Ataka, Yoriko Sawano, Masaru Tanokura
    Quality improvement of protein crystals in a high magnetic field Topics award!
    Japan Society for Bioscience, Biotechnology, and Agrochemistry Annual Meeting of JSBBA 2012 (Oral) March 22-25(24), 2012
    Kyoto Women's University, Kyoto, Japan.

  17. You-Lin Xue, Takuya Miyakawa, Akira Nakamura, Yoriko Sawano, Masaru Tanokura
    Cloning of genes and enzymatic characterizations of novel dioscorin isoforms from Dioscorea japonica
    Japan Society for Bioscience, Biotechnology, and Agrochemistry Annual Meeting of JSBBA 2012 (Oral) March 22-25(24), 2012
    Kyoto Women's University, Kyoto, Japan.

  18. Akira Nakamura, Jun Ohtsuka, Ken-ichi Miyazono, Akihiro Yamamura, Keiko Kubota, Ryoichi Hirose, Tatsuki Kashiwagi, Eiichiro Suzuki, Noriyuki Hirota, Hitoshi Wada, Mitsuo Ataka, Yoriko Sawano, Masaru Tanokura
    Protein Crystallization in a high gradient magnetic field
    5th International Workshop on Materials Analysis and Processing in Magnetic Fields (MAP5) (Oral) May 13-17(15), 2012
    Escandille Resort and Convention Center, Autrans, France.

  19. Huimin Qin, Takuya Miyakawa, Akira Nakamura, Takashi Kawashima, Makoto Hibi, Jun Ogawa, Masaru Tanokura
    Crystal Structure of a Novel Branched-Chain Amino Acid Dioxygenase from Burkholderia ambifaria AMMD
    American Crystallographic Association, Inc. Annual Meeting (Poster) July 28-August 1(Jul.29), 2012
    The Westin Boston Waterfront, Boston, MA, USA.

  20. Takaaki Sato, Akira Nakamura, Riku Aono,Masahiro Fujihashi,Yosuke Nishiba, Shosuke Yoshida, Ayumu Yano, Tadayuki Imanaka, Kunio Miki, Haruyuki Atomi
    Dynamic, ligand-dependent conformational change triggers the reaction of ribose-1,5-bisphosphate isomerase from Thermococcus kodakarensis
    The International Society for Extremophiles 9th International Congress on Extremophiles (Poster) September 10-13, 2012
    NH Central Convenciones, Sevilla, Spain.

  21. Xuan Shi, Takuya Miyakawa, Akira Nakamura, Feng Hou, Makoto Hibi, Jun Ogawa, Masaru Tanokura
    X-ray crystallography of AMKP reductases useful for 4-HIL synthesis
    Japan Society for Bioscience, Biotechnology, and Agrochemistry Annual Meeting of JSBBA 2013 (Oral) March 25-27(25), 2013
    Tohoku University, Sendai, Japan.

  22. Akira Nakamura, Atsuko Asano, Takuya Miyakawa, Yoriko Sawano, Yoh Sakuma, Junya Mizoi, Kazuko Yamaguchi-Shinozaki, Masaru Tanokura
    Crystal structure of a plant abiotic stress-responsive transcription factor, DREB2A
    Japan Society for Bioscience, Biotechnology, and Agrochemistry Annual Meeting of JSBBA 2013 (Oral) March 25-27(25), 2013
    Tohoku University, Sendai, Japan.

  23. Akira Nakamura, Jun Ohtsuka, Masaru Tanokura
    Protein crystallization and observation of crystal growth in a magnetic field.
    4th International Symposium on Diffraction Structural Biology (ISDSB2013)(Poster) May 26-29(28), 2013
    Nagoya Trade & Industry Center (Fukiage Hall), Nagoya, Japan.

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Presentations at Other Meeting

  1. Akira Nakamura, Hirofumi Komori, Gengo Kobayashi, Chieko Wada, Kunio Miki
    Crystallization of mini-F plasmid replication initiator protein RepE N-terminal domain dimer.
    Biological Machinery The 5th Workshop (Poster) July 15-17, 2002
    Hotel New AKAO, Shizuoka, Japan

  2. Akira Nakamura, Hirofumi Komori, Gengo Kobayashi, Akiko Kita,Chieko Wada, Kunio Miki
    Crystallization of replication initiator protein RepE dimerization domain
    Life of Proteins Group Meeting (Poster) January 13-16, 2004
    Otsu Prince Hotel, Shiga, Japan

  3. Akira Nakamura, Chieko Wada, Kunio Miki
    X-ray crystallographic analysis of the F-plasmid replication initiator protein RepE
    -Implications for understanding an activation mechanism of RepE by the DnaK molecular chaperone system-
    Life of Proteins Post Symposium (Poster) November 22-23, 2007
    Atami New Fujiya Hotel, Shizuoka, Japan

  4. Akira Nakamura, Kouhei Takumi, Kunio Miki
    Structural basis for the thermosensing function of a cochaperone GrpE in the DnaK system from Thermus thermophilus HB8
    PF Symposium The 26th Symposium (Poster) March 24-25(25), 2009
    Tsukuba International Congress Center (EPOCHAL TSUKUBA)

  5. Akira Nakamura, Masahiro Fujihashi, Yosuke Nishiba, Shosuke Yoshida, Ayumu Yano, Haruyuki Atomi, Tadayuki Imanaka, Kunio Miki
    Crystal structure analysis of ribose-1,5-bisphosphate isomerase of the novel carbon fixation pathway in a hyperthermophilic archaeon.
    PF Symposium The 27th Symposium (Poster) March 09-10(9), 2010
    Tsukuba International Congress Center (EPOCHAL TSUKUBA)

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Academic Society Affiliations

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[Kyoto Univ.] [Grad. Sch. Sci.] [Dept. Chem.] [Biol. Struct. Chem.] [Miki Group] [Members]