J Oda

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. ncbi Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase
    T Nakatsu
    Institute for Chemical Research, Kyoto University, Japan
    Nat Struct Biol 5:15-9. 1998
  2. ncbi Flexible loop that is novel catalytic machinery in a ligase. Atomic structure and function of the loopless glutathione synthetase
    H Kato
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 33:4995-9. 1994
  3. ncbi Flexibility impaired by mutations revealed the multifunctional roles of the loop in glutathione synthetase
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 32:12398-404. 1993
  4. ncbi Site-directed mutagenesis of glutathione synthetase from Escherichia coli B: mapping of the gamma-L-glutamyl-L-cysteine-binding site
    T Hara
    Institute for Chemical Research, Kyoto University, Japan
    Protein Eng 8:711-6. 1995
  5. ncbi Nicked multifunctional loop of glutathione synthetase still protects the catalytic intermediate
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Arch Biochem Biophys 339:151-6. 1997
  6. ncbi A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution
    T Hara
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 35:11967-74. 1996
  7. ncbi Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins
    K Matsuda
    Institute for Chemical Research, Kyoto University, Japan
    Protein Eng 9:1083-92. 1996
  8. ncbi Use of adenosine (5')polyphospho(5')pyridoxals to study the substrate-binding region of glutathione synthetase from Escherichia coli B
    T Hibi
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 32:1548-54. 1993
  9. ncbi Role of cysteine residues in glutathione synthetase from Escherichia coli B. Chemical modification and oligonucleotide site-directed mutagenesis
    H Kato
    Institute for Chemical Research, Kyoto University, Japan
    J Biol Chem 263:11646-51. 1988
  10. ncbi [Structural and functional analysis on glutathione-synthetase]
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Tanpakushitsu Kakusan Koso 38:1579-88. 1993

Collaborators

Detail Information

Publications19

  1. ncbi Crystal structure of asparagine synthetase reveals a close evolutionary relationship to class II aminoacyl-tRNA synthetase
    T Nakatsu
    Institute for Chemical Research, Kyoto University, Japan
    Nat Struct Biol 5:15-9. 1998
    ..The functional and structural similarities of both enzymes suggest that new enzymatic activities would generally follow the recruitment of a protein catalyzing a similar chemical reaction...
  2. ncbi Flexible loop that is novel catalytic machinery in a ligase. Atomic structure and function of the loopless glutathione synthetase
    H Kato
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 33:4995-9. 1994
    ..These studies support the fact that the loop enhances the recognition of glycine as well as stabilizes the acyl phosphate intermediate so that the intermediate rapidly reacts with glycine...
  3. ncbi Flexibility impaired by mutations revealed the multifunctional roles of the loop in glutathione synthetase
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 32:12398-404. 1993
    ..The present results suggest that adjustability of the loop to the closed state is required for the recognition of the substrates, gamma-Glu-Cys and glycine, and for the chemical interactions with the bound substrates...
  4. ncbi Site-directed mutagenesis of glutathione synthetase from Escherichia coli B: mapping of the gamma-L-glutamyl-L-cysteine-binding site
    T Hara
    Institute for Chemical Research, Kyoto University, Japan
    Protein Eng 8:711-6. 1995
    ..The other mutant enzymes showed little defect in their kinetic parameters of gamma-Glu-Cys...
  5. ncbi Nicked multifunctional loop of glutathione synthetase still protects the catalytic intermediate
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Arch Biochem Biophys 339:151-6. 1997
    ..In conclusion, it is postulated that the two fragments of the nicked loop independently assumed the closed state to protect the catalytic intermediate and have lost the ability to accelerate glutathione synthesis...
  6. ncbi A pseudo-michaelis quaternary complex in the reverse reaction of a ligase: structure of Escherichia coli B glutathione synthetase complexed with ADP, glutathione, and sulfate at 2.0 A resolution
    T Hara
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 35:11967-74. 1996
    ..Functional aspects of the active site architecture in the substrate-binding form are discussed...
  7. ncbi Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins
    K Matsuda
    Institute for Chemical Research, Kyoto University, Japan
    Protein Eng 9:1083-92. 1996
    ..A structural motif in the N-terminal domain of GSHase has been found to be similar to the NAD-binding fold. This structural motif is shared by a number of other proteins that bind various negatively charged molecules...
  8. ncbi Use of adenosine (5')polyphospho(5')pyridoxals to study the substrate-binding region of glutathione synthetase from Escherichia coli B
    T Hibi
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 32:1548-54. 1993
    ..These results demonstrate the bivalent binding of AP4-PL lying across the gamma-glutamylcysteine- and ATP-binding sites...
  9. ncbi Role of cysteine residues in glutathione synthetase from Escherichia coli B. Chemical modification and oligonucleotide site-directed mutagenesis
    H Kato
    Institute for Chemical Research, Kyoto University, Japan
    J Biol Chem 263:11646-51. 1988
    ..Replacement of Cys-122 to Ala-122 enhanced the reactivity of Cys-289 with sulfhydryl reagents...
  10. ncbi [Structural and functional analysis on glutathione-synthetase]
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Tanpakushitsu Kakusan Koso 38:1579-88. 1993
  11. ncbi Crystallization and preliminary X-ray studies of glutathione synthetase from Escherichia coli B
    H Kato
    Institute for Chemical Research, Kyoto University, Japan
    J Mol Biol 209:503-4. 1989
    ..0 A, c = 164.2 A, and gamma = 120 degrees. The enzyme is a tetramer (Mr = 143,000) with 222 symmetry, and the asymmetric unit contains one subunit molecule (Mr = 35,600). The crystals diffract to at least 2.5 A resolution...
  12. ncbi ATP-dependent inactivation of Escherichia coli gamma-glutamylcysteine synthetase by L-glutamic acid gamma-monohydroxamate
    M Katoh
    Institute for Chemical Research, Kyoto University, Japan
    Biosci Biotechnol Biochem 62:1455-7. 1998
    ....
  13. ncbi Overexpression and purification of asparagine synthetase from Escherichia coli
    A Sugiyama
    Institute for Chemical Research, Kyoto University
    Biosci Biotechnol Biochem 56:376-9. 1992
    ..Furthermore the native molecular weight measured by gel filtration confirmed that asparagine synthetase exists as a dimer of identical subunits...
  14. ncbi Purification, molecular cloning, and expression of lipase from Pseudomonas aeruginosa
    M Chihara-Siomi
    Institute for Chemical Research, Kyoto University, Japan
    Arch Biochem Biophys 296:505-13. 1992
    ..Expression plasmids encoding lipA followed by the complete or incomplete lipB gene downstream of the lac promoter of pUC18 were constructed. lipA was expressed in Escherichia coli 1100 only in the presence of the complete lipB gene...
  15. ncbi Mutational and proteolytic studies on a flexible loop in glutathione synthetase from Escherichia coli B: the loop and arginine 233 are critical for the catalytic reaction
    T Tanaka
    Institute for Chemical Research, Kyoto University, Japan
    Biochemistry 31:2259-65. 1992
    ..These results suggest that the loop covers the active site while ATP and gamma-Glu-Cys bind there and that it protects the unstable gamma-Glu-Cys phosphate intermediate from decomposition by bulk water.(ABSTRACT TRUNCATED AT 250 WORDS)..
  16. ncbi Design, synthesis and evaluation of transition-state analogue inhibitors of Escherichia coli gamma-glutamylcysteine synthetase
    N Tokutake
    Institute for Chemical Research, Kyoto University, Japan
    Bioorg Med Chem 6:1935-53. 1998
    ..The sulfoximine with (S)-sulfur was a simple reversible inhibitor with an inhibition potency comparable to that of the sulfone. The synthesis and inhibition profile of the N-phosphoryl sulfoximine is also described...
  17. ncbi Structure of the multifunctional loops in the nonclassical ATP-binding fold of glutathione synthetase
    T Hibi
    Nat Struct Biol 3:16-8. 1996
  18. ncbi Three-dimensional structure of the glutathione synthetase from Escherichia coli B at 2.0 A resolution
    H Yamaguchi
    Institute for Protein Research Osaka University, Japan
    J Mol Biol 229:1083-100. 1993
    ..The ATP binding site is surrounded by two sets of the structural motif that belong to those respective domains. Each motif consists of an anti-parallel beta-sheet and a glycine-rich loop...
  19. ncbi Homology of Escherichia coli B glutathione synthetase with dihydrofolate reductase in amino acid sequence and substrate binding site
    H Kato
    J Biochem 101:207-15. 1987
    ..coli B enzyme provides the ATP binding site. This report gives experimental evidence that amino acid sequences related by sequence homology conserve functional similarity even in enzymes which differ in their catalytic mechanisms...