S Kamitori

Summary

Affiliation: Tokyo University of Agriculture and Technology
Country: Japan

Publications

  1. ncbi request reprint Crystal structure of chartreusin derivative A132
    Shigehiro Kamitori
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    Carbohydr Res 338:1523-5. 2003
  2. ncbi request reprint Crystal structures of Aspergillus oryzae aspartic proteinase and its complex with an inhibitor pepstatin at 1.9A resolution
    Shigehiro Kamitori
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    J Mol Biol 326:1503-11. 2003
  3. ncbi request reprint Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution
    Shigehiro Kamitori
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    J Mol Biol 318:443-53. 2002
  4. ncbi request reprint Crystal structures of cyclomaltohexaose (alpha-cyclodextrin) complexes with p-bromophenol and m-bromophenol
    S Kamitori
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Japan
    Carbohydr Res 332:235-40. 2001
  5. ncbi request reprint Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution
    S Kamitori
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184 8588
    J Mol Biol 287:907-21. 1999
  6. ncbi request reprint Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins
    S Kondo
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka-cho, Koganei, Tokyo 184-8588, Japan
    J Biochem 129:423-8. 2001
  7. ncbi request reprint The deletion of amino-terminal domain in Thermoactinomyces vulgaris R-47 alpha-amylases: effects of domain N on activity, specificity, stability and dimerization
    T Yokota
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
    Biosci Biotechnol Biochem 65:401-8. 2001
  8. ncbi request reprint Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues
    T Yokota
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
    Biosci Biotechnol Biochem 65:619-26. 2001
  9. ncbi request reprint Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutan
    A Ohtaki
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, 184-8588, Tokyo, Japan
    Carbohydr Res 334:309-13. 2001
  10. ncbi request reprint Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft
    Akashi Ohtaki
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    Carbohydr Res 341:1041-6. 2006

Collaborators

  • Michio Takeuchi
  • Takashi Tonozuka
  • K Okuyama
  • Atsushi Nishikawa
  • Ken Izumori
  • Keiko Kita
  • Masafumi Yohda
  • Hiromi Yoshida
  • Yoshiyuki Sakano
  • Masahiro Mizuno
  • Akashi Ohtaki
  • Mitsugu Yamada
  • Goro Takada
  • Akemi Abe
  • Kazuhiro Ichikawa
  • Y Sakano
  • T Yokota
  • Yuma Kurakata
  • Takeyori Nishitani
  • A Ohtaki
  • S Kondo
  • Akiko Uechi
  • Yoshinori Imai
  • Shinichi Kohsaka
  • Yusuke Oku
  • Y Shimura
  • Atsushi Koide
  • Hiromi Akeboshi
  • Akihiro Yamamura
  • Yuya Ohyama
  • Keiko Ohsawa
  • Poonperm Wayoon
  • Yoshihiro Tanabe
  • Yutaka Kawarabayasi
  • Rie Uotsu-Tomita
  • Saori Suzuki
  • Hiroyuki Ohno
  • Nobuhumi Nakamura
  • Akihiro Iguchi
  • K Ichikawa

Detail Information

Publications28

  1. ncbi request reprint Crystal structure of chartreusin derivative A132
    Shigehiro Kamitori
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    Carbohydr Res 338:1523-5. 2003
    ..A modeling study of the A132-DNA complex based on the X-ray structures suggests that the sugar moiety of A132 may play an important role in recognizing the sequence of DNA base pairs...
  2. ncbi request reprint Crystal structures of Aspergillus oryzae aspartic proteinase and its complex with an inhibitor pepstatin at 1.9A resolution
    Shigehiro Kamitori
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    J Mol Biol 326:1503-11. 2003
    ..The X-ray structure of AOAP/pepstatin complex and preliminary modeling show two possible sites of recognition for the positively charged groups of Lys/Arg residues around the active site of AOAP...
  3. ncbi request reprint Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution
    Shigehiro Kamitori
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    J Mol Biol 318:443-53. 2002
    ..A structural comparison of the active sites has clearly revealed this difference in substrate specificity...
  4. ncbi request reprint Crystal structures of cyclomaltohexaose (alpha-cyclodextrin) complexes with p-bromophenol and m-bromophenol
    S Kamitori
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Japan
    Carbohydr Res 332:235-40. 2001
    ..The intermolecular hydrogen-bond interactions of the hydroxyl groups of bromophenols are closely related to the molecular packing structure...
  5. ncbi request reprint Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution
    S Kamitori
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, Koganei, Tokyo, 184 8588
    J Mol Biol 287:907-21. 1999
    ..The active-site cleft of TVAII is wider and shallower than that of other alpha-amylases, and seems to be suitable for the binding of pullulan which is expected not to adopt the helical structure of amylose...
  6. ncbi request reprint Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins
    S Kondo
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Naka-cho, Koganei, Tokyo 184-8588, Japan
    J Biochem 129:423-8. 2001
    ..These studies also suggested that the TVAII-hydrolyzing mechanism for cyclodextrins is slightly different from that for starch...
  7. ncbi request reprint The deletion of amino-terminal domain in Thermoactinomyces vulgaris R-47 alpha-amylases: effects of domain N on activity, specificity, stability and dimerization
    T Yokota
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
    Biosci Biotechnol Biochem 65:401-8. 2001
    ..These results suggest domain N in TVAs is an important structure for stabilization of enzymes, recognition and hydrolysis of substrates, and dimerization of TVA II...
  8. ncbi request reprint Structures of Thermoactinomyces vulgaris R-47 alpha-amylase II complexed with substrate analogues
    T Yokota
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu-shi, Japan
    Biosci Biotechnol Biochem 65:619-26. 2001
    ..These results suggest that the lack of the residues related to alpha-glucan and CD-stacking causes the functional distinctions between CGTase and TVA II...
  9. ncbi request reprint Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutan
    A Ohtaki
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, 184-8588, Tokyo, Japan
    Carbohydr Res 334:309-13. 2001
    ....
  10. ncbi request reprint Structure of a complex of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with maltohexaose demonstrates the important role of aromatic residues at the reducing end of the substrate binding cleft
    Akashi Ohtaki
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    Carbohydr Res 341:1041-6. 2006
    ....
  11. ncbi request reprint X-ray structures of the microglia/macrophage-specific protein Iba1 from human and mouse demonstrate novel molecular conformation change induced by calcium binding
    Mitsugu Yamada
    Information Technology Center and Faculty of Medicine, Kagawa University, 1750 1 Ikenobe, Miki cho, Kita gun, Kagawa 761 0793, Japan
    J Mol Biol 364:449-57. 2006
    ....
  12. ncbi request reprint The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity
    Hiromi Yoshida
    Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750 1 Ikenobe, Miki cho, Kita gun, Kagawa 761 0793, Japan
    J Mol Biol 365:1505-16. 2007
    ..stutzeri L-RhI, there is no corresponding hydrophobic pocket where Phe66 from a neighbouring molecule merely forms hydrophobic interactions with the substrate, leading to the loose substrate recognition at the 4, 5, and 6 positions...
  13. pmc Purification, crystallization and preliminary X-ray diffraction studies of D-tagatose 3-epimerase from Pseudomonas cichorii
    Hiromi Yoshida
    Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750 1 Ikenobe, Miki cho, Kita gun, Kagawa 761 0793, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:123-5. 2007
    ..80, b = 94.92, c = 91.73 A, beta = 102.82 degrees . Diffraction data were collected to 2.5 A resolution. The asymmetric unit is expected to contain four molecules...
  14. ncbi request reprint Structural basis for cyclodextrin recognition by Thermoactinomyces vulgaris cyclo/maltodextrin-binding protein
    Takashi Tonozuka
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Japan
    FEBS J 274:2109-20. 2007
    ..These findings suggest that the sugar-binding site of the N-domain part and the wide cleft are critical in determining the specificity of TvuCMBP for gamma-cyclodextrin...
  15. ncbi request reprint Crystal structures of D-tagatose 3-epimerase from Pseudomonas cichorii and its complexes with D-tagatose and D-fructose
    Hiromi Yoshida
    Life Science Research Center and Faculty of Medicine, Kagawa University, 1750 1 Ikenobe, Miki cho, Kita gun, Kagawa 761 0793, Japan
    J Mol Biol 374:443-53. 2007
    ..Furthermore, a C3-O3 proton-exchange mechanism for P. cichoriid-TE is suggested by X-ray structural analysis, providing a clear explanation for the regulation of the ionization state of Glu152 and Glu246...
  16. ncbi request reprint Crystal structure of Aspergillus niger isopullulanase, a member of glycoside hydrolase family 49
    Masahiro Mizuno
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3 5 8 Saiwai cho, Fuchu, Tokyo 183 8509, Japan
    J Mol Biol 376:210-20. 2008
    ..The shape of the catalytic cleft characterized by the seventh coil of the beta-helix and a loop from domain N appears to be critical in determining the specificity of IPU for pullulan...
  17. pmc Crystallization and preliminary X-ray analysis of Thermoactinomyces vulgaris R-47 maltooligosaccharide-metabolizing enzyme homologous to glucoamylase
    Kazuhiro Ichikawa
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183 8509, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:302-4. 2005
    ..Gel-filtration and native PAGE analyses indicated that TGA exists as a dimer in solution. This is the first report of the crystallization of an oligomeric glucoamylase...
  18. ncbi request reprint Complexes of Thermoactinomyces vulgaris R-47 alpha-amylase 1 and pullulan model oligossacharides provide new insight into the mechanism for recognizing substrates with alpha-(1,6) glycosidic linkages
    Akemi Abe
    Graduate School of Medicine, Kagawa University, Japan
    FEBS J 272:6145-53. 2005
    ..In this study, additional substrates were also found to bind to domain N, suggesting that domain N also functions as a pullulan-binding domain...
  19. ncbi request reprint X-ray structures of NADPH-dependent carbonyl reductase from Sporobolomyces salmonicolor provide insights into stereoselective reductions of carbonyl compounds
    Shigehiro Kamitori
    Molecular Structure Research Group, Information Technology Center, Kagawa University, 1750 1 Ikenobe, Miki cho, Kita gun, Kagawa 791 0793, Japan
    J Mol Biol 352:551-8. 2005
    ..The X-ray structure of the SSCR/NADPH complex and preliminary modeling show that the formation of the hydrophobic channel induced by the binding of NADPH is closely related to the stereoselective reduction by SSCR...
  20. ncbi request reprint Mutual conversion of substrate specificities of Thermoactinomyces vulgaris R-47 alpha-amylases TVAI and TVAII by site-directed mutagenesis
    Akashi Ohtaki
    Department of Biotechnology and Life Science, Faculty of Technology, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    Carbohydr Res 338:1553-8. 2003
    ....
  21. ncbi request reprint Structural insights into substrate specificity and function of glucodextranase
    Masahiro Mizuno
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo 183 8509, Japan
    J Biol Chem 279:10575-83. 2004
    ..The primary structure of domain C is homologous with a surface layer homology domain of pullulanases, and the three-dimensional structure of domain C resembles the carbohydrate-binding domain of some glycohydrolases...
  22. ncbi request reprint Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 1 with malto-oligosaccharides demonstrate the role of domain N acting as a starch-binding domain
    Akemi Abe
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    J Mol Biol 335:811-22. 2004
    ..An assay of hydrolyzing activity for the raw starches confirmed that TVAI can efficiently hydrolyze raw starch...
  23. ncbi request reprint Crystallization and preliminary X-ray crystallographic analysis of macrophage/microglia-specific calcium-binding protein Iba1
    Mitsugu Yamada
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    Acta Crystallogr D Biol Crystallogr 60:569-71. 2004
    ..28, b = 44.06, c = 99.13 A, beta = 90.03 degrees for mouse Iba1. Both crystals diffracted well to a resolution of 2.1 A and initial phase determinations were attempted by a molecular-replacement method using calmodulin structures...
  24. ncbi request reprint Complex structures of Thermoactinomyces vulgaris R-47 alpha-amylase 2 with acarbose and cyclodextrins demonstrate the multiple substrate recognition mechanism
    Akashi Ohtaki
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2 24 16 Naka cho, Koganei, Tokyo 184 8588, Japan
    J Biol Chem 279:31033-40. 2004
    ..From the x-ray structures, it is suggested that the protonation of the O-4 atom is possibly carried out via a hydrogen atom of the inter-glucose hydrogen bond at the hydrolyzing site...
  25. ncbi request reprint The crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) complexed with transglycosylated product
    Masahiro Mizuno
    Department of Applied Biological Science, Tokyo Univrsity of Agriculture and Technology, Tokyo, Japan
    Eur J Biochem 271:2530-8. 2004
    ....
  26. ncbi request reprint Structure and direct electrochemistry of cytochrome P450 from the thermoacidophilic crenarchaeon, Sulfolobus tokodaii strain 7
    Yusuke Oku
    Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184 8588, Japan
    J Inorg Biochem 98:1194-9. 2004
    ..A quasi-reversible redox response has been observed even at elevated temperatures of up to 80 degrees C...
  27. doi request reprint Structural insights into the substrate specificity and function of Escherichia coli K12 YgjK, a glucosidase belonging to the glycoside hydrolase family 63
    Yuma Kurakata
    Department of Applied Biological Science, Tokyo University of Agriculture and Technology, 3 5 8 Saiwai cho, Fuchu, Tokyo 183 8509, Japan
    J Mol Biol 381:116-28. 2008
    ..These findings suggest that YgjK is a glucosidase with relaxed specificity for sugars...
  28. pmc Crystallization and preliminary X-ray diffraction studies of L-rhamnose isomerase from Pseudomonas stutzeri
    Hiromi Yoshida
    Molecular Structure Research Group, Information Technology Center and Faculty of Medicine, Kagawa University, 1750 1 Ikenobe, Miki cho, Kita gun, Kagawa 761 0793, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:550-2. 2006
    ..0 A resolution. The molecular weight of the purified P. stutzeri L-RhI with a His tag at the C-terminus was confirmed to be 47.7 kDa by MALDI-TOF mass-spectrometric analysis and the asymmetric unit is expected to contain four molecules...