| 1.Research Institution | Osaka Medical College | |
| 2.Research Area | Life Sciences | |
| 3.Research Field | Structure and Functional Control Mechanism of Biomolecules | |
| 4.Term of Project | FY1996〜FY2000 | |
| 5.Project Number | 96L00506 | |
| 6.Title of Project | Exploring the steric superfine structures and dynamics as the basis of substrate recognition and catalysis of multifunctional enzymes |
| Name | Institution,Department | Title of Position |
| Hiroyuki Kagamiyama | Osaka Medical College, Biochemistry | Professer |
8.Core Members
| Names | Institution,Department | Title of Position |
| Hideyuki Hayashi | Osaka Medical College, Biochemistry | Associate Professor |
9.Cooperating Researchers
| Names | Institution,Department | Title of Position |
| Ken Hirotsu | Osaka City Univ. Graduate School of Science | Professor |
| Retsu Miura | Kumamoto Univ. School of Medicine | Professor |
| Tetsuo Toraya | Okayama Univ. Engineering | Professor |
10.Summary of Research Results
|
In this project, the three dimensional structures of pyridoxal enzymes (10), flavin enzymes (2), a cobalamin enzyme, and a quinoenzyme have been analyzed. Based on the structures, substrate-recognition and reaction mechanisms of these enzymes have been studied in detail, and important new findings were obtained. 1) A new concept for enzyme catalysis was presented. Enzymes are charged with strain energy, mainly found in the structures formed between the coenzymes and the enzyme proteins in their unliganded forms, and release the strain energy on binding of substrates, thereby reducing the activation energy barrier and enhancing the catalytic efficiency and stereoselectivity. The conformational changes of the enzymes responsible for the release of the strains have been elucidated structurally. 2) Quantum-chemical interpretation of the proton-transfer and electron-transfer process clarified how the enzyme protein controls the reaction specificity. In many enzymes, the reaction mechanism has been revised based on these findings of this project, which could not have been obtained by conventional methods of enzymology. 3) Several enzymes were found to undergo reorganization of the active site to accept different kinds of substrates, while maintaining the rigid structure of the part facing the reaction center. Based on this principle, substrate specificity could be altered by directed evolution using auxotrophy and DNA shuffling. The same strategy was successfully applied to develop a thermostable enzyme. 4) The process of formation of the prosthetic group (built-in coenzyme) has been elucidated at the atomic level. Other findings are as follows. 5) Discovery and gene cloning of a protein that catalyzes the energy-dependent replacement of the inactivated coenzyme in the enzyme with the intact adenosylcobalamin. 6) Isolation and gene cloning of enzymes from psychrophiles. X-ray structural analyses are under way to elucidate how these enzymes are active at low temperatures. |
11.Key Words
(1)Pyridoxal enzymes 、(2)Flavin enzymes、(3)Cobalamin enzymes
(4)Build-in coenzymes、(5)Substrat recognition、(6)Enzyme-reaction mechanism
(7)X-ray crystallography、(8)Molecular design of active site、(9)Directed evolution
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| Protein Engineering | 11 | 1998 | 613-619 | |
| Author | Title of Article | |||
| Uo, T. | Occurrence Of Pyridoxal 5'-Phosphate-Dependent Serine Racemase in Silkworm, Bombyx mori. | |||
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| Author | Title of Article | |||
| Li, Y. -F | X-Ray Structure of A Reaction Intermediate of L-2-Haloacid Dehalogenase with L-2-Chloropropionamide. | |||
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| J. Biochem. | 124 | 1998 | 20-22 | |
| Author | Title of Article | |||
| Nishina, Y. | Resonance Raman Study on Reduced Flavin in Purple Intermediate of Flavoenzyme: Use of [4-Carbonyl-18O]-Enriched Flavin. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 124 | 1998 | 200-208 | |
| Author | Title of Article | |||
| Matsuzaki, R. | Exploring A Channel to The Active Site of Copper / Topaquinone-Containing Phenylethylamine Oxidase by Chemical. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 37 | 1998 | 13947-13957 | |
| Author | Title of Article | |||
| Oue, S. | Redesignning The Substrate Specificity of An Enzyme by Cumulative Effects of The Mutations of Non-Active Site Residues. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 274 | 1999 | 2344-2349 | |
| Author | Title of Article | |||
| Toraya, T. | A Reactivating Factor for Coenzyme B12-Dependent Diol Dehydratase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 247 | 1999 | 3372-3377 | |
| Author | Title of Article | |||
| Watanabe, A. | Role of Lysine39 of Alanine Racemase from Bacillus Stearothermophilus That Binds Pyridoxal 5'-Phosphate:Chemical Rescue Studies of Lys39→Ala Mutant. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 247 | 1999 | 4189-4194 | |
| Author | Title of Article | |||
| Tamaoki, H. | Mechanism for Recognition and Activation of Substrate in Medium-Chain Acyl-CoA Dehydrogenase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 125 | 1999 | 285-296 | |
| Author | Title of Article | |||
| Odagaki, Y. | Crystal Structure of The Pyroglutamyl Peptidase I from Bacillus amyloliquefaciens Reveals New Structure for A Cysteine Protease | |||
| Journal | Volume | Year | Pages Concerned | |
| Structure | 7 | 1999 | 399-411 | |
| Author | Title of Article | |||
| Galkin, A. | Cold-Adapted Alanine Dehydrogenases from Two Antarctic Bacterial Strains: Gene Cloning. Protein Characterization, and Comparison with Mesophilic and Thermophilic Counterparts. | |||
| Journal | Volume | Year | Pages Concerned | |
| Appl. Environ. Microbiol. | 65(9) | 1999 | 4014-4020 | |
| Author | Title of Article | |||
| Mihara, H. | AnifS-like Gene, csdB, Encodes an Escherichia coli Counterpart of Mammalian Selenocysteine Lyase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 274(21) | 1999 | 14768-14772 | |
| Author | Title of Article | |||
| Watanabe, A. | Tyrosine 265 of Alanine Racemase Serves as a Base Abstracting a-Hydrogen from L-Alanine: The Counterpart Residue to Lysine 39 Specific to D-Alanine. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 126(4) | 1999 | 781-786 | |
| Author | Title of Article | |||
| Tamaoki, H. | Mechanism for recognition and activation of substrate in medium-chain acyl-CoA dehydrogenase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 125 | 1999 | 285-296 | |
| Author | Title of Article | |||
| Hirota, S. | Spectroscopic Characterzation of Carbon Monoxide Complexes Generated for Copper/Topa Quinone-Containing Amine Oxidases. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 38 | 1999 | 14256-14263 | |
| Author | Title of Article | |||
| Tanizawa, K. | Built-in coenzymes:amino acid residue-derived new coenzyme. | |||
| Journal | Volume | Year | Pages Concerned | |
| Tanpakushittsu ･ Kakusan ･ Kohso | 44 | 1999 | 1947-1958 | |
| Author | Title of Article | |||
| Yamada, K. | Heterologous High-level Expression, Purification, and Enzymological Properties of Recombinant Rat Cobalamin-dependent Methionine Synthase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 274 | 1999 | 35571-35576 | |
| Author | Title of Article | |||
| Mori, K. | The Mechanism of Reactivation of Coenzyme B12-Dependent Diol Dehydratase by a Molecular Chaperone-Like Reactivating Factor. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 38 | 1999 | 13170-13178 | |
| Author | Title of Article | |||
| Toraya, T. | Direct Participaton of Potassium Ion in the Catalysis of Coenzyme B12-Dependent Diol Dehydratase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 126 | 1999 | 650-654 | |
| Author | Title of Article | |||
| Masuda, J. | Crystallization and Preliminary X-ray Study of Two Crystal Forms of Klebsiella oxytoca Diol Dehydratase-cyanocobalamin Complex. | |||
| Journal | Volume | Year | Pages Concerned | |
| Acta. Crystallogr. | D55 | 1999 | 907-909 | |
| Author | Title of Article | |||
| Shibata, N. | A New Mode of B12 Binding and the Direct Particpation of a Potassium Ion in Enzyme Catalysis. X-ray Structure of Diol Dehydratase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Structure | 7 | 1999 | 997-1008 | |
| Author | Title of Article | |||
| Tobimatsu, T. | Identification and Expression of the Genes Encoding a Reactivating Factor for Adenosylcobalamin-dependent Glycerol Dehydratase. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Bacter. | 181 | 1999 | 4410-4113 | |
| Author | Title of Article | |||
| Oikawa, T. | Production of D-Glutamate from L-Glutamate with Glutamate Racemase and L-Glutamate Oxidase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biosci. Biotech. Biochem. | 63 | 1999 | 2168-2173 | |
| Author | Title of Article | |||
| Oikawa, T. | Stereoisomers of Glutathione: Preparation and Enzymatic Reactivities. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Nutr. Sci. Vitaminol. | 45 | 1999 | 223-229 | |
| Author | Title of Article | |||
| Nakai, T. | Structure of Thermus thermophilus HB8 Aspartate Aminotransferase and Its Complex with Maleate. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 38(8) | 1999 | 2413-2424 | |
| Author | Title of Article | |||
| Hoseki, J. | Directed Evolution of Thermostable Kanamycin-Resistant Gene Products in an Extremely Thermophilic Bacterium, Thermus thermophilus. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 126(5) | 1999 | 951-956 | |
| Author | Title of Article | |||
| Hayashi, H. | Acid-Base Chemistry of the Reaction. of Aromatic L-Amino Acid Decarboxylase and Dopa Analyzed by Transient and Steady-State Kinetics: Preferential Binding of the Substrate with Its Amino Group Unprotonated. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 38 | 1999 | 15615-15622 | |
| Author | Title of Article | |||
| Oue, S. | Cocrystallization of a Mutant Aspartate Aminotransferase with a C5-Dicarboxylic Substrate Analog: Structural Comparison with the Enzyme-C4-Dicarboxylic Analog Complex. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 127 | 2000 | 337-343 | |
| Author | Title of Article | |||
| Koyanagi, T. | Molecular Cloning snd Heterologous Expression of Pea Seedling Copper Amine Oxidase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biosci. Biotech. Biochem. | 64 | 2000 | 717-722 | |
| Author | Title of Article | |||
| Mihara, H. | Kinetic and mutational studies of three Nifs homologs from Escherichia coli : Mechanistic difference between L-cysteine desulfurase and L-selenocysteine lyase reactions. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 127(2) | 2000 | 559-567 | |
| Author | Title of Article | |||
| Mihara, H. | cDNA cloning, purification, and characterization of mouse liver selenocysteine lyase. Condidate for selenium delivery protein in selenoprotein synthesis. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 275(9) | 2000 | 6195-6200 | |
| Author | Title of Article | |||
| Fujii, T. | Structure of Nifs homologue: X-ray structure analysis of Csd B, an Escherichia coli counterpart of mammalian selenocysteine lyase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 39(6) | 2000 | 1263-1273 | |
| Author | Title of Article | |||
| Gutierrez, A. | Modulation of activity and substrate specificity by modifying the backbone length of the distant interdomain loop of D-amino acid aminotransferase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Eur. J. Biochem. | 267(24) | 2000 | 7218-7223 | |
| Author | Title of Article | |||
| Nakai, T. | Three dimensional structure of 4-amino-4-deoxychorismate lyase from Escherichia coli. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 128 | 2000 | 29-38 | |
| Author | Title of Article | |||
| Jhee, K. -H. | Stereochemistry of the transamination reaction catalyzed by aminodeoxychorismate lyase from Escherichia coli: Close relationship between fold type and stereochemistry. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 128(4) | 2000 | 679-686 | |
| Author | Title of Article | |||
| Ishijima, J. | Free energy requirement for domain movement of enzyme. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 275(25) | 2000 | 18939-18945 | |
| Author | Title of Article | |||
| Matsui, I. | The molecular structure of hyperthermostable aromatic aminotransferase with novel substrate specificity from Pyrococcus horikoshii. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biol. Chem. | 275(7) | 2000 | 4871-4879 | |
| Author | Title of Article | |||
| Mizutani, H. | Three-dimensional structure of the purple intermediate of porcine kidney D-amino acid oxidase. Optimization of the oxidative half-reaction through alignment of the product with reduced flavin. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 128 | 2000 | 73-81 | |
| Author | Title of Article | |||
| Toraya, T. | Radical atalysis of B12 enzymes: structure, mechanism, inactivation and reactivation of diol and glycerol dehydratasesm. | |||
| Journal | Volume | Year | Pages Concerned | |
| Cell. Mol. Life Sci. | 57 | 2000 | 106-127 | |
| Author | Title of Article | |||
| Masuda, J. | How a grotein generates a catalytic radical from coenzyme B12 : X-ray structure of a diol - dehydratase - adeninylpentylcobalamin Complex. | |||
| Journal | Volume | Year | Pages Concerned | |
| Structure | 8 | 2000 | 775-788 | |
| Author | Title of Article | |||
| Tobimatsu, T. | Specificities of reactivating factors for adenosylcoblamin - dependent diol dehydratase and glycerol dehydratase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Arch. Microbiol. | 174 | 2000 | 81-88 | |
| Author | Title of Article | |||
| Nishina, Y. | Substrate recognition and activation mechanism of D-amino acid oxidase : A study using substrate analogs. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 128 | 2000 | 213-223 | |
| Author | Title of Article | |||
| M. M. Islam | The substrate activation process in the catalytic reaction of Escherichia coli aromatic amino acid aminotransferase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 39(50) | 2000 | 15418-15428 | |
| Author | Title of Article | |||
| Kagamiyama, H. | Studies of transaminases on the basis of their tertiary structures | |||
| Journal | Volume | Year | Pages Concerned | |
| Vitamins | 74(1) | 2000 | 1-12 | |
| Author | Title of Article | |||
| Ura, H. | Temperature dependence of the enzyme - substrate recognition mechanism. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Biochem. | 129(1) | 2001 | 173-178 | |
| Author | Title of Article | |||
| Mizuguchi, H. | Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspatate aminotransferase. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 40 | 2001 | 353-360 | |
| Author | Title of Article | |||
| Miura, R. | Porcine kidney D-amino acid oxidase : The three dimensional structure and its catalytic mechanism based on the enzyme - substrate complex model. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Mol. Catalysis. B, Enzymatic | 12 | 2001 | 43-52 | |
| Author | Title of Article | |||
| Haruyama, K. | Structure of Escherichia coli histidinol - phosphate aminotransferase and its complexes with histidinol - phosphate and N-(5'-phosphopyridoxyl)-L-glutamate double substrate recognition of the enzyme | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochemistry | 40 | 2001 | in press | |
| Author | Title of Article | |||
| Miura, R. | Versatility and specificity of flavoenzymes : Control mechanism of flavin reactivity. | |||
| Journal | Volume | Year | Pages Concerned | |
| The Chemical Record | 1 | 2001 | in press | |
| Author | Title of Article | |||
| Watanabe, A. | Stereochemistry of the hydrogen abstraction from pyridoxamine phosphate catalyzed by alanine racemase of Bacillus stearothermophilus. | |||
| Journal | Volume | Year | Pages Concerned | |
| J. Mol. Catalysis | 2001 | in press | ||
| Author | Title of Article | |||
| Eda, M. | Theoretical Predictions on the Mechanism of Catalysis of Coenzyme B12 - Dependent Diol. | |||
| Journal | Volume | Year | Pages Concerned | |
| Dehydratase | 2001 | in press | ||
| Author | Title of Article | |||
| Oikawa, T. | Fragmentary form of thermostable leucine dehydrogenase of Bacillus stearothermophilus: Its construction and reconstruction of active fragmentary enzyme. | |||
| Journal | Volume | Year | Pages Concerned | |
| Biochem. Biophys. Res. Commun | 2001 | in press | ||
| Author | Title of Article | |||
| Oikawa, T. | Alanine aminotransferase II from the hyperthermophilic archaeon Thermococcus sp. TK1: Purification, molecular characterization, and expression in Escherichia coli. | |||
| Journal | Volume | Year | Pages Concerned | |
| Eur, J. Biochem. | 2001 | in press | ||
| Author | Title of Article | |||
| Oikawa, T. | Psychrophilic valine dehydrogenase of Antarctic Psychophile, Cytophaga sp. P1: Purification, molecular characterization, and expression in Escherichia coli. | |||
| Journal | Volume | Year | Pages Concerned | |
| Eur. J. Biochem. | 2001 | |||
| Author | Title of Article | |||
| Kazuoka, T. | Thermostable alcohol dehydrogenase from a Psycophile, Cytophage sp. KUC-1: Cloning, molecular characterization. | |||
| Journal | Volume | Year | Pages Concerned | |
| Proc. Natl. Acad. Sci. USA | 2001 | in press | ||
| Author | Title of Article | |||
| Oikawa, T | Alanine aminotransferase I from the hyperthermophilic Archaeon Thermococcus sp. TK1: Purification, molecular characterization, and expression in Escherichia coli. | |||
| Journal | Volume | Year | Pages Concerned | |
| Eur. J. Biochem. | 2001 | in press | ||
| Author | Title of Book | ||
| Miura, R. | Flavins and Flavoproteins | ||
| Publisher | Year | Pages | |
| Agency for Scientific Publ., Berlin. | 1999 | 939 | |
| Author | Title of Book | ||
| Setoyama, C. | Flavins and Flavoproteins | ||
| Publisher | Year | Pages | |
| Agency for Scientific Publ., Berlin. | 1999 | 939 | |
| Author | Title of Book | ||
| Kagamiyama, H. | Methodes in Enzymology (Branched. chain amino acid aminotransferase in E. coli) | ||
| Publisher | Year | Pages | |
| Academic Press | 2000 | 550 | |
| Author | Title of Book | ||
| Hayashi, H. | Biochemistry and Molecular Bioligy of Vitamin B6 and PQQ - dependent proteins | ||
| Publisher | Year | Pages | |
| Birkhauser Verlag | 2000 | 376 | |
| Author | Title of Book | ||
| Hirotsu, K. | Biochemistry and Molecular Biology of Vitamin B6 and PQQ - dependent proteins. | ||
| Publisher | Year | Pages | |
| Birkhauser Verlag | 2000 | 376 | |