Kazuhiko Yamasaki

Summary

Affiliation: National Institute of Advanced Industrial Science and Technology
Country: Japan

Publications

  1. ncbi request reprint Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    J Mol Biol 348:253-64. 2005
  2. doi request reprint Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    Plant Physiol Biochem 46:394-401. 2008
  3. doi request reprint DNA-binding domains of plant-specific transcription factors: structure, function, and evolution
    Kazuhiko Yamasaki
    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    Trends Plant Sci 18:267-76. 2013
  4. pmc Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor
    Kazuhiko Yamasaki
    National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    J Biol Chem 287:7683-91. 2012
  5. doi request reprint Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases
    Kazuhiko Yamasaki
    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    FEBS Lett 584:3370-5. 2010
  6. ncbi request reprint An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    FEBS Lett 580:2109-16. 2006
  7. pmc Solution structure of an Arabidopsis WRKY DNA binding domain
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 17:944-56. 2005
  8. ncbi request reprint A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Insitute of Advanced Industrial Science and Technology, Tsukuba, Japan
    J Mol Biol 337:49-63. 2004
  9. ncbi request reprint Acid-induced denaturation of Escherichia coli ribonuclease HI analyzed by CD and NMR spectroscopies
    Kazuhiko Yamasaki
    National Institute of Advanced Industrial Science and Technology, 1 1 1, Higashi, Tsukuba, 305 8566, Japan
    Biopolymers 69:176-88. 2003
  10. pmc Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 16:3448-59. 2004

Detail Information

Publications26

  1. ncbi request reprint Solution structure of the major DNA-binding domain of Arabidopsis thaliana ethylene-insensitive3-like3
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    J Mol Biol 348:253-64. 2005
    ..The structure consists of five alpha-helices, possessing a novel fold dissimilar to known DBD structures. By a chemical-shift perturbation analysis, a region including the ein3-3 site is suggested to be involved in DNA binding...
  2. doi request reprint Structures and evolutionary origins of plant-specific transcription factor DNA-binding domains
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    Plant Physiol Biochem 46:394-401. 2008
    ....
  3. doi request reprint DNA-binding domains of plant-specific transcription factors: structure, function, and evolution
    Kazuhiko Yamasaki
    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    Trends Plant Sci 18:267-76. 2013
    ..After the DBDs have been established in unicellular eukaryotes, they experienced extensive plant-specific expansion, by acquiring new functions...
  4. pmc Structural basis for sequence-specific DNA recognition by an Arabidopsis WRKY transcription factor
    Kazuhiko Yamasaki
    National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    J Biol Chem 287:7683-91. 2012
    ..The importance of these contacts was verified by substituting the relevant T bases with U and by surface plasmon resonance analyses of DNA binding...
  5. doi request reprint Solution structure of the N-terminal domain of the archaeal D-family DNA polymerase small subunit reveals evolutionary relationship to eukaryotic B-family polymerases
    Kazuhiko Yamasaki
    Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    FEBS Lett 584:3370-5. 2010
    ..We observed monomer-dimer equilibrium of this domain, which may be related to holoenzyme architecture and/or functional regulation...
  6. ncbi request reprint An Arabidopsis SBP-domain fragment with a disrupted C-terminal zinc-binding site retains its tertiary structure
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    FEBS Lett 580:2109-16. 2006
    ....
  7. pmc Solution structure of an Arabidopsis WRKY DNA binding domain
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 17:944-56. 2005
    ..Based on a profile of NMR chemical shift perturbations, we propose that the same strand enters the DNA groove and forms contacts with the DNA bases...
  8. ncbi request reprint A novel zinc-binding motif revealed by solution structures of DNA-binding domains of Arabidopsis SBP-family transcription factors
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Insitute of Advanced Industrial Science and Technology, Tsukuba, Japan
    J Mol Biol 337:49-63. 2004
    ..The electrostatic profile on the surface suggested that a continuous region, including all the conserved basic residues, is involved in the DNA binding, the mode of which is likely to be novel as well...
  9. ncbi request reprint Acid-induced denaturation of Escherichia coli ribonuclease HI analyzed by CD and NMR spectroscopies
    Kazuhiko Yamasaki
    National Institute of Advanced Industrial Science and Technology, 1 1 1, Higashi, Tsukuba, 305 8566, Japan
    Biopolymers 69:176-88. 2003
    ..The profile of hydrogen-bond protection indicated that the structure of the A-state is closely related to that of the kinetic folding intermediate...
  10. pmc Solution structure of the B3 DNA binding domain of the Arabidopsis cold-responsive transcription factor RAV1
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba 305 8566, Japan
    Plant Cell 16:3448-59. 2004
    ..The locations of the DNA-contacting residues are also likely to be similar to those of the EcoRII DNA binding domain...
  11. ncbi request reprint Cell-free synthesis of zinc-binding proteins
    Takayoshi Matsuda
    Protein Research Group, RIKEN Genomic Sciences Center, 1 7 22 Suehiro cho, Tsurumi, Yokohama 230 0045, Japan
    J Struct Funct Genomics 7:93-100. 2006
    ..NMR analyses confirmed that correctly folded proteins were synthesized by the cell-free method. These results indicate that the cell-free method can be used to synthesize correctly folded and functional zinc-binding proteins...
  12. doi request reprint Glycerol stimulates innate chaperoning, proteasomal and stress-resistance functions: implications for geronto-manipulation
    Custer C Deocaris
    National Institute of Advanced Industrial Science and Technology AIST, Central 4, 1 1 1 Higashi, Tsukuba, 305 8562, Japan
    Biogerontology 9:269-82. 2008
    ..These results may have significant implications in the use of glycerol as a candidate geronto-modulator in development of practical interventions for "healthy aging"...
  13. ncbi request reprint Structural and sequence comparisons arising from the solution structure of the transcription elongation factor NusG from Thermus thermophilus
    Paul Reay
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Proteins 56:40-51. 2004
    ....
  14. pmc Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB1
    Kazuhiko Yamasaki
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Nucleic Acids Res 35:5073-84. 2007
    ....
  15. ncbi request reprint Stress chaperones, mortalin, and pex19p mediate 5-aza-2' deoxycytidine-induced senescence of cancer cells by DNA methylation-independent pathway
    Nashi Widodo
    National Institute of Advanced Industrial Science and Technology AIST, Central 4, 1 1 1, Higashi, Tsukuba, Ibaraki, Japan
    J Gerontol A Biol Sci Med Sci 62:246-55. 2007
    ..We conclude that both mortalin and Pex19p are important mediators, prognostic indicators, and tailoring tools for 5AZA-dC-induced senescence in cancer cells...
  16. ncbi request reprint Solution structure and DNA-binding mode of the matrix attachment region-binding domain of the transcription factor SATB1 that regulates the T-cell maturation
    Hiroshi Yamaguchi
    Age Dimension Research Center, National Institute of Advanced Industrial Science and Technology, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    J Biol Chem 281:5319-27. 2006
    ..These observations suggested that SATB1 possesses a DNA-binding mode similar to that of the POU-specific DNA-binding domain, which is known to share structural similarity to the four-helix CUT domain...
  17. ncbi request reprint Mortalin sensitizes human cancer cells to MKT-077-induced senescence
    Custer C Deocaris
    National Institute of Advanced Industrial Science and Technology AIST, Central 4, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8562, Japan
    Cancer Lett 252:259-69. 2007
    ..Our work may likely translate to a re-appraisal of the therapeutic benefits of low doses of several classes of anti-tumor drugs, even of those that had been discontinued due to adverse effects...
  18. ncbi request reprint Nature of the chemical bond formed with the structural metal ion at the A9/G10.1 motif derived from hammerhead ribozymes
    Yoshiyuki Tanaka
    Gene Function Research Center, National Institute of Advanced Industrial Science and Technology, Central 4, 1 1 1 Higashi, Tsukuba Science City 305 8562, Japan
    J Am Chem Soc 126:744-52. 2004
    ..This observation suggests that the metal ion at these motifs is not a catalytic center of hammerhead ribozymes...
  19. ncbi request reprint Geroprotection by glycerol: insights to its mechanisms and clinical potentials
    Custer C Deocaris
    National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Ann N Y Acad Sci 1067:488-92. 2006
    ..This was accompanied by decrease in p53, an upregulation of a stress chaperone mortalin/mtHsp70, and an increase in proteasome activity in the presence of oxidative stress...
  20. ncbi request reprint Molecular structure and novel DNA binding sites located in loops of flap endonuclease-1 from Pyrococcus horikoshii
    Eriko Matsui
    Biological Information Research Center and the Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology, Higashi 1 1 1, Tsukuba, Ibaraki 305 566, Japan
    J Biol Chem 277:37840-7. 2002
    ..For the exo-activity, all four sites were needed, but Arg(118)-Lys(119) was dominant. The major binding sites for both the nick substrate and double-stranded DNA might be the same...
  21. ncbi request reprint A modified sensor chip for surface plasmon resonance enables a rapid determination of sequence specificity of DNA-binding proteins
    Dongyun Hao
    National Institute of Advanced Industrial Science and Technology, 1 1 1 Higashi, Tsukuba 305 8566, Japan
    FEBS Lett 536:151-6. 2003
    ..The time necessary for one cycle is approximately 50 min, which is shorter than existing methods...
  22. doi request reprint Effect of glycosylation on cis/trans isomerization of prolines in IgA1-hinge peptide
    Yoshiki Narimatsu
    Research Center for Medical Glycoscience RCMG, National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Ibaraki, Japan
    J Am Chem Soc 132:5548-9. 2010
    ..The appropriate glycosylation of HP probably contributes to the decrease in the unfavorable variety of relative orientations between Fab and Fc in IgA1, through stabilizing the conformation of HP...
  23. ncbi request reprint 10 residue folded peptide designed by segment statistics
    Shinya Honda
    National Institute of Advanced Industrial Science and Technology, AIST Central 6, Tsukuba 305 8566, Japan
    Structure 12:1507-18. 2004
    ..This is of interest for the pursuit of folding mechanisms and evolutionary processes of proteins...
  24. ncbi request reprint Structural and functional differences between mouse mot-1 and mot-2 proteins that differ in two amino acids
    Custer C Deocaris
    National Institute of Advanced Industrial Science and Technology AIST, Tsukuba, Japan
    Ann N Y Acad Sci 1067:220-3. 2006
    ..Here, we provide evidence that mot-1 possesses very low chaperone activity as compared to mot-2. A "lazy lid" hypothesis is proposed for their differential aging phenotypes...
  25. ncbi request reprint Identification of the metal ion binding site on an RNA motif from hammerhead ribozymes using (15)N NMR spectroscopy
    Yoshiyuki Tanaka
    Gene Discovery Research Center, National Institute of Advanced Industrial Science and Technology, Tsukuba Central 4, 1 1 1 Higashi, Tsukuba, Ibaraki 305 8562, Japan
    J Am Chem Soc 124:4595-601. 2002
    ..This is the first experimental evidence to prove that the N7/G7 binds with a Cd(II) ion...
  26. ncbi request reprint Determinants in the sequence specific binding of two plant transcription factors, CBF1 and NtERF2, to the DRE and GCC motifs
    Dongyun Hao
    Gene Discovery Research Centre, National Institute of Advanced Industrial Science and Technology AIST, Central 6, Tsukuba 305 8566, Japan
    Biochemistry 41:4202-8. 2002
    ..This demonstrates that A14 is an important determinant of the NtERF2-F binding specificity. A possible mechanism of the binding specificity determination is discussed...