Ken Hirotsu

Summary

Affiliation: Osaka City University
Country: Japan

Publications

  1. ncbi request reprint Dual substrate recognition of aminotransferases
    Ken Hirotsu
    Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    Chem Rec 5:160-72. 2005
  2. ncbi request reprint Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen
    Keiji Tokuoka
    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi ku, Osaka 558 8585
    J Biochem 139:789-95. 2006
  3. ncbi request reprint Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism
    Rie Omi
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 278:46035-45. 2003
  4. ncbi request reprint Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
    Atsuko Satoh
    Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi ku, Osaka 558 8585
    J Biochem 134:297-304. 2003
  5. ncbi request reprint Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 278:22964-71. 2003
  6. ncbi request reprint Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 280:40875-84. 2005
  7. ncbi request reprint Crystal structures of branched-chain amino acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi ku, Osaka 558 8585 Japan
    Biochemistry 42:3725-33. 2003
  8. ncbi request reprint Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 279:16518-25. 2004
  9. ncbi request reprint Crystal structures of CTP synthetase reveal ATP, UTP, and glutamine binding sites
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560 0043, Japan
    Structure 12:1413-23. 2004
  10. pmc Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 284:25944-52. 2009

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Dual substrate recognition of aminotransferases
    Ken Hirotsu
    Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    Chem Rec 5:160-72. 2005
    ..Dual substrate recognition in other aminotransferases is attained by combining the two representative methods...
  2. ncbi request reprint Three-dimensional structure of rat-liver acyl-CoA oxidase in complex with a fatty acid: insights into substrate-recognition and reactivity toward molecular oxygen
    Keiji Tokuoka
    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi ku, Osaka 558 8585
    J Biochem 139:789-95. 2006
    ....
  3. ncbi request reprint Crystal structures of threonine synthase from Thermus thermophilus HB8: conformational change, substrate recognition, and mechanism
    Rie Omi
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 278:46035-45. 2003
    ....
  4. ncbi request reprint Structure of the transition state analog of medium-chain acyl-CoA dehydrogenase. Crystallographic and molecular orbital studies on the charge-transfer complex of medium-chain acyl-CoA dehydrogenase with 3-thiaoctanoyl-CoA
    Atsuko Satoh
    Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi ku, Osaka 558 8585
    J Biochem 134:297-304. 2003
    ..The structure of the highest occupied molecular orbital of the complex revealed the electron flow pathway from a substrate to the flavin ring...
  5. ncbi request reprint Structures of argininosuccinate synthetase in enzyme-ATP substrates and enzyme-AMP product forms: stereochemistry of the catalytic reaction
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 278:22964-71. 2003
    ..The stereochemistry of the catalysis of the enzyme is clarified on the basis of the structures of tAsS (argininosuccinate synthetase from T. thermophilus HB8) complexes...
  6. ncbi request reprint Crystal structures of Delta1-piperideine-2-carboxylate/Delta1-pyrroline-2-carboxylate reductase belonging to a new family of NAD(P)H-dependent oxidoreductases: conformational change, substrate recognition, and stereochemistry of the reaction
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 280:40875-84. 2005
    ..The active site structure of the catalytic form made it possible to identify the catalytic Asp:Ser:His triad and investigate the catalytic mechanism from a stereochemical point of view...
  7. ncbi request reprint Crystal structures of branched-chain amino acid aminotransferase complexed with glutamate and glutarate: true reaction intermediate and double substrate recognition of the enzyme
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi ku, Osaka 558 8585 Japan
    Biochemistry 42:3725-33. 2003
    ..In the histidinol-phosphate aminotransferase, the acidic and basic side chains are located at different sites and interact with different residues of the disordered loop...
  8. ncbi request reprint Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 279:16518-25. 2004
    ..The inner side of the pocket is mostly hydrophobic, but also has polar sites. The kynurenine complex generated by computer modeling fits the pocket of the enzyme and its hydrophilic groups interact with the polar sites of the pocket...
  9. ncbi request reprint Crystal structures of CTP synthetase reveal ATP, UTP, and glutamine binding sites
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560 0043, Japan
    Structure 12:1413-23. 2004
    ..Structural information provides an insight into the conformational changes associated with the binding of ATP and UTP and the formation of the GTP binding site...
  10. pmc Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 284:25944-52. 2009
    ....
  11. ncbi request reprint Expression, purification and preliminary X-ray characterization of histidinol phosphate phosphatase
    Rie Omi
    Department of Chemistry, Graduate School of Science, Osaka City University, Japan
    Acta Crystallogr D Biol Crystallogr 60:574-6. 2004
    ..57 A(3) Da(-1) for form I and 2.96 A(3) Da(-1) for form II. X-ray data have been collected to 1.70 and 1.75 A resolution for crystal forms I and II, respectively...
  12. ncbi request reprint Structural determinants for branched-chain aminotransferase isozyme-specific inhibition by the anticonvulsant drug gabapentin
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 280:37246-56. 2005
    ..The structural data suggest that there is a larger effect of oxidation on the interdomain loop and residues surrounding the CXXC center in hBCATm than in hBCATc...
  13. ncbi request reprint Three-dimensional structure of the flavoenzyme acyl-CoA oxidase-II from rat liver, the peroxisomal counterpart of mitochondrial acyl-CoA dehydrogenase
    Yoshitaka Nakajima
    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi ku, Osaka 558 8585, Japan
    J Biochem 131:365-74. 2002
    ..The crevice for binding the fatty acyl chain is 28 A long and 6 A wide, large enough to accommodate the C23 acyl chain...
  14. ncbi request reprint Expression, purification and preliminary X-ray characterization of CTP synthetase from Thermus thermophilus HB8
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Japan
    Acta Crystallogr D Biol Crystallogr 59:551-3. 2003
    ..The crystals obtained from ammonium sulfate and sodium citrate solutions diffract X-rays to a resolution of 2.25 A using synchrotron X-ray sources and to a resolution of 2.35 A using Cu Kalpha X-rays from a rotating-anode generator...
  15. ncbi request reprint Structure of imidazole glycerol phosphate synthase from Thermus thermophilus HB8: open-closed conformational change and ammonia tunneling
    Rie Omi
    Department of Chemistry, Graduate School of Science, Osaka City University, Sugimoto, Sumiyoshi ku, Osaka 558 8585
    J Biochem 132:759-65. 2002
    ....
  16. ncbi request reprint The active site structure of quinohemoprotein amine dehydrogenase inhibited by p-nitrophenylhydrazine
    Atsuko Satoh
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    Biochim Biophys Acta 1647:272-7. 2003
    ..The inhibitor may have access to the active site pocket through the water-filled crevice between the beta- and gamma-subunits...
  17. ncbi request reprint Expression, purification and preliminary X-ray characterization of N-acetyl-gamma-glutamyl-phosphate reductase from Thermus thermophilus HB8
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Sumiyoshi ku, Osaka 558 8585, Japan
    Acta Crystallogr D Biol Crystallogr 59:356-8. 2003
    ..19 A(3) Da(-1). The crystals diffract to a resolution of 2.2 A at beamline BL44B2 of SPring-8...
  18. ncbi request reprint Crystal structure of argininosuccinate synthetase from Thermus thermophilus HB8. Structural basis for the catalytic action
    Masaru Goto
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 277:15890-6. 2002
    ..The reaction mechanism so far proposed seems to be consistent with the locations of ATP and the substrate analogues. The reaction may proceed without the large conformational change of the enzyme proposed for the catalytic process...
  19. ncbi request reprint Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges
    Atsuko Satoh
    Department of Chemistry, Graduate School of Science, Osaka City University, Osaka 558 8585, Japan
    J Biol Chem 277:2830-4. 2002
    ..Thus, the structure of the 79-residue gamma-subunit is quite unusual, containing four internal cross-links in such a short polypeptide chain that would otherwise be difficult to fold into a globular structure...
  20. ncbi request reprint Crystal structures of nonoxidative zinc-dependent 2,6-dihydroxybenzoate (gamma-resorcylate) decarboxylase from Rhizobium sp. strain MTP-10005
    Masaru Goto
    Department of Biochemistry, Osaka Medical College, Takatsuki, Osaka 569 8686, Japan
    J Biol Chem 281:34365-73. 2006
    ..On the basis of the geometrical consideration, substrate specificity is uncovered, and the catalytic mechanism is proposed for the novel Zn2+-dependent decarboxylation...
  21. ncbi request reprint Effects of hydrogen bonds in association with flavin and substrate in flavoenzyme d-amino acid oxidase. The catalytic and structural roles of Gly313 and Thr317
    Chiaki Setoyama
    Department of Biochemistry, Kumamoto University School of Medicine, Honjo, Kumamoto 860 0811, Japan
    J Biochem 131:59-69. 2002
    ....
  22. ncbi request reprint Binding of C5-dicarboxylic substrate to aspartate aminotransferase: implications for the conformational change at the transaldimination step
    Mohammad Mainul Islam
    Department of Biochemistry, Osaka Medical College, 2 7 Daigakumachi, Takatsuki 569 8686, Japan
    Biochemistry 44:8218-29. 2005
    ..The hydrophobic residues of the entrance of the active site, including Tyr70, are considered to be important for promoting the transaldimination process and hence the recognition of the C5 substrate...
  23. ncbi request reprint Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis
    Hideyuki Hayashi
    Department of Biochemistry, Osaka Medical College, Takatsuki 569 8686, Japan
    J Biol Chem 278:9481-8. 2003
    ..Kinetic analysis suggested that the repulsion increases the free energy level of the Michaelis complex and promotes the catalytic reaction...
  24. ncbi request reprint Mechanism of preferential enrichment, an unusual enantiomeric resolution phenomenon caused by polymorphic transition during crystallization of mixed crystals composed of two enantiomers
    Rui Tamura
    Gradutate School of Human and Environmental Studies, Kyoto University, Kyoto 606 8501, Japan
    J Am Chem Soc 124:13139-53. 2002
    ..Both metastable and stable crystals have been obtained, and their crystal structures have been elucidated by X-ray crystallographic analysis of their single crystals...
  25. pmc Crystallization screening test for the whole-cell project on Thermus thermophilus HB8
    Hitoshi Iino
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo cho, Sayo gun, Hyogo 679 5148, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:487-91. 2008
    ..The structures of 360 of 944 purified proteins have been successfully determined through the combined use of an HTS-80 and a TERA...
  26. ncbi request reprint Crystal structure of monofunctional histidinol phosphate phosphatase from Thermus thermophilus HB8
    Rie Omi
    RIKEN SPring 8 Center, Harima Institute, 1 1 1 Kouto, Sayo, Hyogo 679 5148, Japan
    Biochemistry 46:12618-27. 2007
    ....
  27. pmc Expression, purification and preliminary X-ray characterization of DL-2-haloacid dehalogenase from Methylobacterium sp. CPA1
    Rie Omi
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:586-9. 2007
    ..20-2.10 A3 Da(-1). A self-rotation function revealed peaks on the chi = 180 degrees section. X-ray data have been collected to 1.75 A resolution...
  28. ncbi request reprint Characterization of histidinol phosphate aminotransferase from Escherichia coli
    Hiroyuki Mizuguchi
    Department of Biochemistry, Osaka Medical College, Takatsuki 569 8686, Japan
    Biochim Biophys Acta 1647:321-4. 2003
    ..Our findings also support the idea that the strain mechanism is common to Subgroup I aminotransferases...
  29. ncbi request reprint Engineering the substrate specificity of porcine kidney D-amino acid oxidase by mutagenesis of the "active-site lid"
    Chiaki Setoyama
    Departments of Molecular Enzymology and Molecular Physiology, Graduate School of Medical Sciences, Kumamoto University, 1 1 1 Honjo, Kumamoto 860 8556
    J Biochem 139:873-9. 2006
    ..The specificity constant, k(cat app)/K(m app), for D-arginine increased by one order of magnitude for the 221D224G or 222D224G mutant, whereas that for D-alanine or D-serine decreased to marginal or nil...
  30. ncbi request reprint A new family of NAD(P)H-dependent oxidoreductases distinct from conventional Rossmann-fold proteins
    Hisashi Muramatsu
    Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    J Biosci Bioeng 99:541-7. 2005
    ..This classification would be useful for reliable functional annotation of the new family of NAD(P)H-dependent oxidoreductases...
  31. ncbi request reprint Glutamine:phenylpyruvate aminotransferase from an extremely thermophilic bacterium, Thermus thermophilus HB8
    Akira Hosono
    Department of Biochemistry, Osaka Medical College, 2 7 Daigakumachi, Takatsuki 569 8686
    J Biochem 134:843-51. 2003
    ..The origin of this unique pKa value and the substrate specificity is discussed based on the previous crystallographic data of T. thermophilus and E. coli aspartate aminotransferases...
  32. ncbi request reprint Strain and catalysis in aspartate aminotransferase
    Hideyuki Hayashi
    Department of Biochemistry, Osaka Medical College, 2 7 Daigaku cho, Takatsuki 569 8686, Japan
    Biochim Biophys Acta 1647:103-9. 2003
    ....