| 1.Research Institution | Osaka University | |
| 2.Research Area | Life Sciences | |
| 3.Research Field | Structure and Functional Control Mechanism of Biomolecules (Structural Biology and Functional Molecules) | |
| 4.Term of Project | FY1996〜FY2000 | |
| 5.Project Number | 96L00503 | |
| 6.Title of Project | Molecular Regulation in Biological Macromolecular Assemblies |
| Name | Institution,Department | Title of Position |
| Tsukihara, Tomitake | Osaka University, Institute for Protein Research | Professor |
8.Core Members
| Names | Institution,Department | Title of Position |
| Nakagawa, Atsushi | Osaka University, Institute for Protein Research | Associate Professor |
| Yamashita, Eiki | Osaka University, Institute for Protein Research | Research Associate |
| Yoshikawa, Shinya | Himeji Institute of Technology, Faculty of Science | Professor |
9.Cooperating Researchers
| Names | Institution,Department | Title of Position |
| Matsugaki, Naohito | Osaka University, Institute for Protein Research | Post-doctoral fellow |
| Chong, Khoon Tee | Osaka University, Institute for Protein Research | Post-doctoral fellow |
10.Summary of Research Results
|
X-ray structures of oxidized enzyme were determined at 2.3 Å resolution and room temperature and at 2.0 Å and 100 K; that of reduced form, at 2.35 Å resolution and room temperature; that of azide-form, at 2.8 Å resolution and room temperature; and that of CO-form, at 2.8 Å resolution and room temperature. An iron and a copper atoms of the dioxygen reduction center were bridged by an peroxide anion at the oxidized state of the enzyme. Copper atom of the dioxygen reduction center was coordinated by three histidine residues. A side chain of one of the histidine ligands had a covalent linkage with a side chain of tyrosine residue. The tyrosine residue had a hydrogen bond with a hydroxy group of heme a3 side chain. Significant structural change was detected at Asp51 of subunit I upon reduction of the enzyme. We proposed that structural change of Asp51 functioned as proton pump. Structural models of Seven 720 subunits of outer capsid exhibiting T=13 icosahedral symmetry and those of 120 subunits of inner core with T=2 symmetry were built in the 3.5 Å electron density map of rice dwarf virus. X-ray structure of a novel bacteriophage was determined at 3.8 Å resolution. X-ray analysis of 20S proteasome from bovine liver elucidated folds of all the 28 subunits. |
11.Key Words
(1)X-ray Crystallography、(2)Cytochrome c Oxidase、(3)Membrane Protein
(4)Rice Dwarf Virus、(5)Double Shelled Virus、(6)Highperthermophilie
(7)Proteasome、(8)Teriary Structure、(9)Respiratory Enzyme
12.References
| Author | Title of Article | |||
| T. Tsukihara, et al. | The Whole Structure of the 13-Subinit Oxidized Cytochrome c Oxidase at 2.8 A. | |||
| Journal | Volume | Year | Pages Concerned | |
| Science | 272 | 1996 | 1136-1144 | |
| Author | Title of Article | |||
| Wallin, E., et al. | Architecture of helix bundle membrane proteins: An analysis of cytochrome c oxidase from bovine mitochondria | |||
| Journal | Volume | Year | Pages Concerned | |
| Protein Science | 6 | 1997 | 808-815 | |
| Author | Title of Article | |||
| T. H. Tahirov, et al. | Crystallization and Preliminary X-ray Analysis of Methionine Aminopeptodase from the Hyperthermophilic Bacterium Pyrococcus furiosus | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta Crystallogr. | D53 | 1997 | 798-801 | |
| Author | Title of Article | |||
| S. Yoshikawa et al. | Redox-Coupled Crystal Structural Change in Bovine Herart Cytochrome c Oxidase | |||
| Journal | Volume | Year | Pages Concerned | |
| Science | 280 | 1998 | 1723-1729 | |
| Author | Title of Article | |||
| T. T. Tahirov et al. | High-Resolution Crystal of Methionine Aminopeptidase from Pyrococcus furiosus Obtained by Water-Mediated Transformation | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Structural Biology | 121 | 1998 | 68-72 | |
| Author | Title of Article | |||
| T. H. Tahirov et al. | Crystal Structure of Methionine Aminopeptidase from Hyperthermophile, Pyrococcus furiosus | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Mol. Biol. | 284 | 1998 | 101-124 | |
| Author | Title of Article | |||
| A. Sanjoh and T. Tsukihara | Spatiotemporal protein crystal growth studies using microfliidic silicon devices | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Crystal Growth | 196 | 1998 | 691-702 | |
| Author | Title of Article | |||
| T. Tsukihara and S. Yoshikawa | Crystal Structural Studies of a Membrane Protein Complex, Cytochrome c Oxidase from Bovine Heart | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta Crystallogr | A54 | 1998 | 895-904 | |
| Author | Title of Article | |||
| H. Sakai and T. Tsukihara | Structures of Membrane Proteins Determined at Atomic Resolution | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochemistry | 124 | 1998 | 1051-1059 | |
| Author | Title of Article | |||
| T. Tsukihara and Soo Jae Lee | Membrane Proteins: Structure and Function | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Synchrotron Rad. | 6 | 1999 | 918-927 | |
| Author | Title of Article | |||
| T. Tomizaki et al. | Crystal Structure Analysis of Bovine Heart Cytochrome c Oxidase at 2.8 A Resolution | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta Crystallogr. | D55 | 1999 | 31-45 | |
| Author | Title of Article | |||
| H. Naitow et al. | A Low Resolution Crystal Structure of Rice Dwarf Virus Determined by Ab initio Phasing | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta Crystallogr. | D55 | 1999 | 77-84 | |
| Author | Title of Article | |||
| M. Mochizuki et al. | Quantitative Reevaluation of the Redox Active Sites of Crystalline Bovine Heart Cytochrome c Oxidase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 274 | 1999 | 33403-33411 | |
| Author | Title of Article | |||
| T. Tsukihara and H. Aoyama | Membrane protei assemblies - toward atomic resolution analysis | |||
| Journal | Volume | Year | Pages Concerned | |
| Current Opinion in Structural Biology | 10 | 2000 | 208-212 | |
| Author | Title of Article | |||
| S. Mitsuhashi et al | Crystallization and preliminary X-ray diffraction studies of b-carbonic anhydrase from the red alga Porphyridium purpureum | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta Cryst. | D56 | 2000 | 210-211 | |
| Author | Title of Article | |||
| S. Mitsuhashi et al | X-ray structure of b-carbonic anhydrase from the red alga, Porphyridium purpureum., reveals a novel catalytic site for CO2 hydration | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 275 | 2000 | 5521-5526 | |
| Author | Title of Article | |||
| M. J. Fei et al., | X-ray structure of azide bound fully oxidized cytrochrome c oxidase from bovineheart muscle at 2.9 A resolution. | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta Cryst. | D56 | 2000 | 529-535 | |
| Author | Title of Article | |||
| Y. Oda et al. | Crystal Structure of Tobacco Necrosis Virus at 2.25 A | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Mol. Biol. | 300 | 2000 | 153-169 | |
| Author | Title of Article | |||
| J. Sedzik and T. Tsukihara | Solubilization of PNS Myelin Membrane Proteins by Detergent. | |||
| Journal | Volume | Year | Pages Concerned | |
| Neuro Report | 11 | 2000 | 2559-2563 | |
| Author | Title of Article | |||
| Y. Tomisugi et al. | New Crystal Forms and Low Resolution Structure Analysis of 20S Proteasomes from Bovine Liver. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 127 | 2000 | 941-943 | |
| Author | Title of Article | |||
| S. J. Lee et al. | The adoption of a twisted structure of importin-beta is essential for the protein-protein interaction required for nuclear transport. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Mol. Biol. | 302 | 2000 | 251-264 | |
| Author | Title of Article | |||
| T. Nakai et al. | Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases. | |||
| Journal | Volume | Year | Pages Concerned | |
| Structure | 8 | 2000 | 729-737 | |
| Author | Title of Article | |||
| T. Matsumoto et al. | Roles of functional loops and the C-terminal segment of a single-stranded DNA binding protein elucidated by X-Ray structure analysis. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 127 | 2000 | 329-335 | |
| Author | Title of Article | |||
| M. Odoko et al. | Optimization of the energy constant of the methionine Sδ-Cε bond for X-PLORrefinement of protein structure. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Appl. Cryst. | 34 | 2001 | 80-81 | |
| Author | Title of Book | ||
| S. Yoshikawa et al. | Oxygen Homeostatis and Its Dynamics, Crystal Structure and Reaction Mechanism of Bovine Heart Cytochrome c Oxidase | ||
| Publisher | Year | Pages | |
| Springer-Verlag Tokyo | 1998 | pp13-23 | |