Kohei Oda

Summary

Affiliation: Kyoto Institute of Technology
Country: Japan

Publications

  1. ncbi request reprint Subsite preferences of pepstatin-insensitive carboxyl proteinases from prokaryotes: kumamolysin, a thermostable pepstatin-insensitive carboxyl proteinase
    K Oda
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Sakyo ku, Kyoto 606 8585, Japan
    J Biochem 128:499-507. 2000
  2. ncbi request reprint Purification and characterization of alkaline serine proteinase from photosynthetic bacterium, Rubrivivax gelatinosus KDDS1
    Kohei Oda
    Department of Applied Biology, Kyoto Institute of Technology, Japan
    Biosci Biotechnol Biochem 68:650-5. 2004
  3. pmc A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases
    Alexander Wlodawer
    Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    BMC Struct Biol 3:8. 2003
  4. doi request reprint Response to Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)"
    Shosuke Yoshida
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Science 353:759. 2016
  5. ncbi request reprint Substrate specificity of alkaline serine proteinase isolated from photosynthetic bacterium, Rubrivivax gelatinosus KDDS1
    Somporn Tanskul
    Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    Biochem Biophys Res Commun 309:547-51. 2003
  6. ncbi request reprint Catalytic residues and substrate specificity of recombinant human tripeptidyl peptidase I (CLN2)
    Hiroshi Oyama
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku
    J Biochem 138:127-34. 2005
  7. ncbi request reprint Catalytic residues and substrate specificity of scytalidoglutamic peptidase, the first member of the eqolisin in family (G1) of peptidases
    Yukiko Kataoka
    Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    FEBS Lett 579:2991-4. 2005
  8. ncbi request reprint A new function of isonitrile as an inhibitor of the Pdr5p multidrug ABC transporter in Saccharomyces cerevisiae
    Shogo Yamamoto
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    Biochem Biophys Res Commun 330:622-8. 2005
  9. ncbi request reprint Purification and characterization of serine proteinase from a halophilic bacterium, Filobacillus sp. RF2-5
    Kazumi Hiraga
    Department of Applied Biology, Faculty of Textile Science, Kyoto, Japan
    Biosci Biotechnol Biochem 69:38-44. 2005
  10. ncbi request reprint Glutamate decarboxylase from Lactobacillus brevis: activation by ammonium sulfate
    Kazumi Hiraga
    Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo ku, Kyoto 606 8585, Japan
    Biosci Biotechnol Biochem 72:1299-306. 2008

Collaborators

  • Somporn Tanskul
  • Somboon Tanasupawat
  • Shigeharu Harada
  • Kenneth K S Ng
  • B M Dunn
  • Shigeru Kunugi
  • Michael N G James
  • Kazumi Hiraga
  • Shosuke Yoshida
  • Hiroshi Oyama
  • Yoshiharu Kimura
  • Yasuhito Maeda
  • Kenji Miyamoto
  • Hironao Yamaji
  • Kiyotsuna Toyohara
  • Toshihiko Takehana
  • Ikuo Taniguchi
  • Shogo Yamamoto
  • Alexander Wlodawer
  • Yoshie Ueno
  • Yasunori Fujimoto
  • Katsumi Takada
  • Yukiko Kataoka
  • Nobuyuki Hamanaka
  • Sirapan Sukontasing
  • Hidekazu Ikeuchi
  • Tomoko Tada
  • Tomoko Fujisawa
  • Sirilak Namwong
  • Masahiko Tsunemi
  • Yasushi Nishikata
  • Takao Suzuki
  • Atsushi Abiko
  • Hiroyuki Fukuda
  • Mi Li
  • Stewart R Durell
  • Kenichi Uchida
  • Takatoshi Hamada
  • Sawao Murao
  • Shin Ogasawara
  • Bret B Beyer

Detail Information

Publications19

  1. ncbi request reprint Subsite preferences of pepstatin-insensitive carboxyl proteinases from prokaryotes: kumamolysin, a thermostable pepstatin-insensitive carboxyl proteinase
    K Oda
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Sakyo ku, Kyoto 606 8585, Japan
    J Biochem 128:499-507. 2000
    ..Thus, the hydrophilic nature of the S(2)' subsite was confirmed to be a distinguishing feature of pepstatin-insensitive carboxyl proteinases from prokaryotes...
  2. ncbi request reprint Purification and characterization of alkaline serine proteinase from photosynthetic bacterium, Rubrivivax gelatinosus KDDS1
    Kohei Oda
    Department of Applied Biology, Kyoto Institute of Technology, Japan
    Biosci Biotechnol Biochem 68:650-5. 2004
    ..Thus, the enzyme from Rvi. gelatinosus KDDS1 was thought to be a serine-type proteinase. This was the first serine proteinase characterized from photosynthetic bacteria...
  3. pmc A model of tripeptidyl-peptidase I (CLN2), a ubiquitous and highly conserved member of the sedolisin family of serine-carboxyl peptidases
    Alexander Wlodawer
    Protein Structure Section, Macromolecular Crystallography Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, USA
    BMC Struct Biol 3:8. 2003
    ..Similar enzymes have been found in the genomic sequences of several species, but neither systematic analyses of their distribution nor modeling of their structures have been previously attempted...
  4. doi request reprint Response to Comment on "A bacterium that degrades and assimilates poly(ethylene terephthalate)"
    Shosuke Yoshida
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Science 353:759. 2016
    ..We provide additional PET depolymerization data that further support several other lines of data showing PET assimilation by growing cells of Ideonella sakaiensis. ..
  5. ncbi request reprint Substrate specificity of alkaline serine proteinase isolated from photosynthetic bacterium, Rubrivivax gelatinosus KDDS1
    Somporn Tanskul
    Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    Biochem Biophys Res Commun 309:547-51. 2003
    ..The optimum pH of the enzyme for this substrate was pH 10.7, and the values of kcat, Km, and kcat/Km were 23.7 s(-1), 15.4 microM, and 1.54 microM(-1) s(-1), respectively...
  6. ncbi request reprint Catalytic residues and substrate specificity of recombinant human tripeptidyl peptidase I (CLN2)
    Hiroshi Oyama
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku
    J Biochem 138:127-34. 2005
    ..TPP-I might have evolved from an ancestral gene in order to cleave, in cooperation with cathepsins, useless proteins in the lysosomal compartment...
  7. ncbi request reprint Catalytic residues and substrate specificity of scytalidoglutamic peptidase, the first member of the eqolisin in family (G1) of peptidases
    Yukiko Kataoka
    Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    FEBS Lett 579:2991-4. 2005
    ..Ki of Ac-FKF-(3S,4S)-phenylstatinyl-LR-NH2 for SGP was 1.2x10(-10) M. Taken together, we can conclude that SGP has not only structural and catalytic novelties but also a unique subsite structure...
  8. ncbi request reprint A new function of isonitrile as an inhibitor of the Pdr5p multidrug ABC transporter in Saccharomyces cerevisiae
    Shogo Yamamoto
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    Biochem Biophys Res Commun 330:622-8. 2005
    ..Thus, it was found that the isonitrile shows a different inhibitory spectrum from that of FK506 and enniatin as a potent inhibitor for Pdr5p, Cdr1p, and Cdr2p...
  9. ncbi request reprint Purification and characterization of serine proteinase from a halophilic bacterium, Filobacillus sp. RF2-5
    Kazumi Hiraga
    Department of Applied Biology, Faculty of Textile Science, Kyoto, Japan
    Biosci Biotechnol Biochem 69:38-44. 2005
    ..This is the first serine proteinase with a moderately thermophilic, NaCl-stable, and NaCl-activatable, and that has a unique substrate specificity at the P2 position of substrates from moderately halophilic bacteria, Filobacillus sp...
  10. ncbi request reprint Glutamate decarboxylase from Lactobacillus brevis: activation by ammonium sulfate
    Kazumi Hiraga
    Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Sakyo ku, Kyoto 606 8585, Japan
    Biosci Biotechnol Biochem 72:1299-306. 2008
    ..Thus the biochemical properties of the GAD from L. brevis IFO12005 were significantly different from those from other sources...
  11. ncbi request reprint Exploring the subsite-structure of vimelysin and thermolysin using FRETS-libraries
    Kohei Oda
    Department of Applied Biology, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    FEBS Lett 579:5013-8. 2005
    ..This hypothesis was confirmed by examining the R215D mutant of vimelysin, which showed a substrate specificity profile intermediate between thermolysin and vimelysin...
  12. doi request reprint New families of carboxyl peptidases: serine-carboxyl peptidases and glutamic peptidases
    Kohei Oda
    Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    J Biochem 151:13-25. 2012
    ..In this review, the background of the findings, and crystal structures, catalytic mechanisms, substrates specificities and distribution of the new peptidase families are described...
  13. ncbi request reprint Synergetic effects of pressure and chemical denaturant on protein unfolding: stability of a serine-type carboxyl protease, kumamolisin
    Yasunori Fujimoto
    Department of Polymer Science and Engineering, Kyoto Institute of Technology, Matsugasaki, Sakyo, 606 8585, Japan
    Biochim Biophys Acta 1764:364-71. 2006
    ....
  14. ncbi request reprint A CLN2-related and thermostable serine-carboxyl proteinase, kumamolysin: cloning, expression, and identification of catalytic serine residue
    Hiroshi Oyama
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    J Biochem 131:757-65. 2002
    ..These results strongly suggest that kumamolysin has a unique catalytic triad consisting of Glu78, Asp82, and Ser278 residues, as previously observed for PSCP...
  15. ncbi request reprint [A novel family of proteinases: structure and function of serine-carboxyl proteinases]
    Kohei Oda
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Sakyo ku, Kyoto 606 8585
    Seikagaku 74:1459-63. 2002
  16. doi request reprint Lactobacillus senmaizukei sp. nov., isolated from Japanese pickle
    Kazumi Hiraga
    Department of Applied Biology, Graduate School of Science and Technology, Kyoto Institute of Technology, Goshokaido cho, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    Int J Syst Evol Microbiol 58:1625-9. 2008
    ..Thus, these data indicate that strain L13(T) represents a novel species of the genus Lactobacillus, for which the name Lactobacillus senmaizukei is proposed. The type strain is L13(T) (=NBRC 103853(T)=TISTR 1847(T))...
  17. doi request reprint A bacterium that degrades and assimilates poly(ethylene terephthalate)
    Shosuke Yoshida
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan Department of Biosciences and Informatics, Keio University, 3 14 1 Hiyoshi, Kohoku Ku, Yokohama, Kanagawa 223 8522, Japan
    Science 351:1196-9. 2016
    ..Both enzymes are required to enzymatically convert PET efficiently into its two environmentally benign monomers, terephthalic acid and ethylene glycol. ..
  18. doi request reprint Bio-functional pickles that reduce blood pressure of rats
    Kohei Oda
    a Kyoto Institute of Technology, Sakyo ku, Kyoto, Japan
    Biosci Biotechnol Biochem 78:882-90. 2014
    ..The new type of pickles could temporarily reduce blood pressure in two types of rats, spontaneously hypertensive rats and NaCl-sensitive model rats. Thus, the newly developed pickles appear to be beneficial for pickle business. ..
  19. ncbi request reprint Enniatin has a new function as an inhibitor of Pdr5p, one of the ABC transporters in Saccharomyces cerevisiae
    Kazumi Hiraga
    Department of Applied Biology, Faculty of Textile Science, Kyoto Institute of Technology, Matsugasaki, Sakyo ku, Kyoto 606 8585, Japan
    Biochem Biophys Res Commun 328:1119-25. 2005
    ..The enniatins did not inhibit the function of Snq2p, a homologue of Pdr5p. Thus, it was found that enniatins are potent and specific inhibitors for Pdr5p, with less toxicities than that of FK506...