Takuji Oyama

Summary

Affiliation: Osaka University
Country: Japan

Publications

  1. pmc Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm
    Takuji Oyama
    The Takara Bio Endowed Division, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology OLABB, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    BMC Struct Biol 9:2. 2009
  2. doi request reprint Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids
    Tsuyoshi Waku
    Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Suita, Osaka, Japan
    J Mol Biol 385:188-99. 2009
  3. pmc The nuclear receptor PPARγ individually responds to serotonin- and fatty acid-metabolites
    Tsuyoshi Waku
    The Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Furuedai, Suita, Osaka, Japan
    EMBO J 29:3395-407. 2010
  4. pmc Purification, crystallization and preliminary X-ray analysis of the ligand-binding domain of human lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1)
    Tomoko Ishigaki
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:524-7. 2005
  5. pmc Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis
    Tomoko Miyata
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    Proc Natl Acad Sci U S A 102:13795-800. 2005
  6. pmc Crystallization and preliminary X-ray analysis of the Pax6 paired domain bound to the Pax6 gene enhancer
    Makoto Ito
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:1009-12. 2005
  7. pmc Architectures of archaeal GINS complexes, essential DNA replication initiation factors
    Takuji Oyama
    Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology OLABB, Osaka 565 0874, Japan
    BMC Biol 9:28. 2011
  8. ncbi request reprint The clamp-loading complex for processive DNA replication
    Tomoko Miyata
    Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka 565 0874, Japan
    Nat Struct Mol Biol 11:632-6. 2004
  9. ncbi request reprint Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL
    Izuru Ohki
    Department of Structural Biology, Biomolecular Engineering Research Institute 6 2 3, Furuedai, Suita, Osaka, 565 0874, Japan
    Structure 13:905-17. 2005
  10. ncbi request reprint Structural insights into the PIP2 recognition by syntenin-1 PDZ domain
    Takuma Sugi
    Department of Molecular Biology, Biomolecular Engineering Research Institute BERI, 6 2 3, Furuedai, Suita, Osaka 565 0874, Japan
    Biochem Biophys Res Commun 366:373-8. 2008

Collaborators

Detail Information

Publications21

  1. pmc Atomic structures and functional implications of the archaeal RecQ-like helicase Hjm
    Takuji Oyama
    The Takara Bio Endowed Division, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology OLABB, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    BMC Struct Biol 9:2. 2009
    ..Elucidation of the DNA unwinding and translocation mechanisms by PfuHjm will require its three-dimensional structure at atomic resolution...
  2. doi request reprint Structural insight into PPARgamma activation through covalent modification with endogenous fatty acids
    Tsuyoshi Waku
    Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Suita, Osaka, Japan
    J Mol Biol 385:188-99. 2009
    ..This study presents the structural basis for the activation and modulation mechanism of PPARgamma through covalent modification with endogenous fatty acids...
  3. pmc The nuclear receptor PPARγ individually responds to serotonin- and fatty acid-metabolites
    Tsuyoshi Waku
    The Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Furuedai, Suita, Osaka, Japan
    EMBO J 29:3395-407. 2010
    ..Collectively, these results suggest a novel agonism, in which PPARγ functions as a multiple sensor in response to distinct metabolites...
  4. pmc Purification, crystallization and preliminary X-ray analysis of the ligand-binding domain of human lectin-like oxidized low-density lipoprotein receptor 1 (LOX-1)
    Tomoko Ishigaki
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:524-7. 2005
    ..4 A. For the monomeric form of the ligand-binding domain, native, heavy-atom derivative and SeMet-derivative crystals have been obtained; their diffraction data have been measured to 3.0, 2.4 and 1.8 A resolution, respectively...
  5. pmc Open clamp structure in the clamp-loading complex visualized by electron microscopic image analysis
    Tomoko Miyata
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    Proc Natl Acad Sci U S A 102:13795-800. 2005
    ..The complex appears to represent the intermediate, where the PCNA ring is kept open before ATP hydrolysis by RFC...
  6. pmc Crystallization and preliminary X-ray analysis of the Pax6 paired domain bound to the Pax6 gene enhancer
    Makoto Ito
    Department of Structural Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:1009-12. 2005
    ..0/3.7 A resolution and belongs to the monoclinic space group P2(1), with unit-cell parameters a = 62.21, b = 70.69, c = 176.03 A, beta = 90.54 degrees. Diffraction data were collected to 3.7 A resolution...
  7. pmc Architectures of archaeal GINS complexes, essential DNA replication initiation factors
    Takuji Oyama
    Laboratory of Protein Organic Chemistry, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology OLABB, Osaka 565 0874, Japan
    BMC Biol 9:28. 2011
    ..Due to the low sequence similarity between the archaeal and eukaryotic GINS subunits, the atomic structures of the archaeal GINS complexes are attracting interest for comparisons of their subunit architectures and organization...
  8. ncbi request reprint The clamp-loading complex for processive DNA replication
    Tomoko Miyata
    Department of Structural Biology, Biomolecular Engineering Research Institute, Suita, Osaka 565 0874, Japan
    Nat Struct Mol Biol 11:632-6. 2004
    ..The atomic structure of PCNA fits well into the closed ring, suggesting that this ternary complex represents a state just after the PCNA ring has closed to encircle the DNA duplex...
  9. ncbi request reprint Crystal structure of human lectin-like, oxidized low-density lipoprotein receptor 1 ligand binding domain and its ligand recognition mode to OxLDL
    Izuru Ohki
    Department of Structural Biology, Biomolecular Engineering Research Institute 6 2 3, Furuedai, Suita, Osaka, 565 0874, Japan
    Structure 13:905-17. 2005
    ..Based on the LDL model structure, possible binding modes of LOX-1 to OxLDL are proposed...
  10. ncbi request reprint Structural insights into the PIP2 recognition by syntenin-1 PDZ domain
    Takuma Sugi
    Department of Molecular Biology, Biomolecular Engineering Research Institute BERI, 6 2 3, Furuedai, Suita, Osaka 565 0874, Japan
    Biochem Biophys Res Commun 366:373-8. 2008
    ..These structural features well explain biological phenomena, which were previously reported for the PIP(2)-mediated PDZ ligand-binding regulation...
  11. doi request reprint Atomic structure of mutant PPARgamma LBD complexed with 15d-PGJ2: novel modulation mechanism of PPARgamma/RXRalpha function by covalently bound ligands
    Tsuyoshi Waku
    The Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, 6 2 3, Furuedai, Suita, Osaka 565 0874, Japan
    FEBS Lett 583:320-4. 2009
    ....
  12. doi request reprint Detecting structural similarity of ligand interactions in the lipid metabolic system including enzymes, lipid-binding proteins and nuclear receptors
    Clara Shionyu-Mitsuyama
    Open Laboratories of Advanced Bioscience and Biotechnology, Institute for Protein Research, Osaka University, 6 2 3, Furuedai, Suita, Osaka 565 0874, Japan
    Protein Eng Des Sel 24:397-403. 2011
    ....
  13. pmc Structural basis for channelling mechanism of a fatty acid beta-oxidation multienzyme complex
    Momoyo Ishikawa
    Biomolecular Engineering Research Institute, Furuedai, Suita, Osaka, Japan
    EMBO J 23:2745-54. 2004
    ..This channelling mechanism could be applied to other beta-oxidation multienzymes, as revealed from the homology model of the human mitochondrial trifunctional enzyme complex...
  14. ncbi request reprint Mutational analysis of Pyrococcus furiosus replication factor C based on the three-dimensional structure
    Sonoko Ishino
    Department of Molecular Biology, Biomolecular Engineering Research Institute, 6 2 3 Furuedai, 565 0874 Suita, Osaka, Japan
    Extremophiles 7:169-75. 2003
    ..These results contribute to our general understanding of the structure-function relationship of the RFC molecule for the clamp-loading event...
  15. pmc Crystal structures of autoinhibitory PDZ domain of Tamalin: implications for metabotropic glutamate receptor trafficking regulation
    Takuma Sugi
    Department of Molecular Biology, Biomolecular Engineering Research Institute, Suita, Osaka, Japan
    EMBO J 26:2192-205. 2007
    ..Our study suggests a novel regulatory mechanism of the PDZ domain, by which Tamalin switches between the trafficking-inhibited and -active forms depending on mGluR association...
  16. pmc Adaptability and selectivity of human peroxisome proliferator-activated receptor (PPAR) pan agonists revealed from crystal structures
    Takuji Oyama
    The Takara Bio Endowed Division, Department of Biomolecular Recognition, Institute for Protein Research, Osaka University, Open Laboratories of Advanced Bioscience and Biotechnology, Suita, Osaka 565 0874, Japan
    Acta Crystallogr D Biol Crystallogr 65:786-95. 2009
    ..The comparison between the two PPARdelta complexes revealed how each ligand exhibits either a ;dual selective' or ;single specific' binding mode...
  17. doi request reprint The 2.8 Å crystal structure of the dynein motor domain
    Takahide Kon
    Institute for Protein Research, Osaka University, 3 2 Yamadaoka, Suita, Osaka 565 0871, Japan
    Nature 484:345-50. 2012
    ..We also identify a long-range allosteric communication pathway between the primary ATPase and the microtubule-binding sites. Our work provides a framework for understanding the mechanism of dynein-based motility...
  18. pmc Crystal structures of copper-depleted and copper-bound fungal pro-tyrosinase: insights into endogenous cysteine-dependent copper incorporation
    Nobutaka Fujieda
    Department of Material and Life Science, Division of Advanced Science and Biotechnology, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871, Japan
    J Biol Chem 288:22128-40. 2013
    ....
  19. ncbi request reprint Crystal structure of the RuvA-RuvB complex: a structural basis for the Holliday junction migrating motor machinery
    Kazuhiro Yamada
    Biomolecular Engineering Research Institute, Suita, Osaka, Japan
    Mol Cell 10:671-81. 2002
    ....
  20. ncbi request reprint Domain architectures and characterization of an RNA-binding protein, TLS
    Yuko Iko
    Biomolecular Engineering Research Institute, 6 2 3 Furuedai, Suita, Osaka 565 0874, Japan
    J Biol Chem 279:44834-40. 2004
    ..0 x 10(-5) m, whereas the RRM domain showed no observable interaction with this RNA. This surprising result implies that the zinc finger domain plays a more predominant role in RNA recognition than the RRM domain...
  21. pmc Mutational and structural analyses of Caldanaerobius polysaccharolyticus Man5B reveal novel active site residues for family 5 glycoside hydrolases
    Takuji Oyama
    Institute for Protein Research, Osaka University, Osaka, Japan
    PLoS ONE 8:e80448. 2013
    ..Using these molecular determinants as a probe allowed us to identify Man5D from Caldicellulosiruptor bescii as a mannanase with minor endo-glucanase activity. ..