Summary of Research Project Results Under the JSPS FY2000
"Research for the future Program"



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

7.Projetct Leader
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

[Reference Articles]
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

[Reference Books]
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


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