Hiroyoshi Matsumura

Summary

Affiliation: Osaka University
Country: Japan

Publications

  1. pmc Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex
    Yusuke Nomura
    Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino shi, Chiba 275 0016, Japan
    Nucleic Acids Res 38:7822-9. 2010
  2. doi request reprint Structure basis for the regulation of glyceraldehyde-3-phosphate dehydrogenase activity via the intrinsically disordered protein CP12
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Structure 19:1846-54. 2011
  3. pmc Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p and its functional implications
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biol Chem 287:26528-38. 2012
  4. doi request reprint Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1, Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 422:75-86. 2012
  5. pmc Approach for growth of high-quality and large protein crystals
    Hiroyoshi Matsumura
    Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    J Synchrotron Radiat 18:16-9. 2011
  6. ncbi request reprint Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1, Yamadaoka, Suita, Osaka 565 0871, Japan
    Proteins 70:592-8. 2008
  7. ncbi request reprint Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI
    Takashi Tadokoro
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Japan
    Biochemistry 46:7460-8. 2007
  8. doi request reprint Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form
    Yuichi Koga
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
    FEBS J 275:2632-43. 2008
  9. ncbi request reprint Structural and mutational analysis of Trypanosoma brucei prostaglandin H2 reductase provides insight into the catalytic mechanism of aldo-ketoreductases
    Kubata Bruno Kilunga
    Department of Molecular Behavioral Biology, Osaka Bioscience Institute, 6 2 4 Furuedai, Suita, Osaka 565 0874, Japan
    J Biol Chem 280:26371-82. 2005
  10. pmc Structure and function of a hexameric copper-containing nitrite reductase
    Masaki Nojiri
    Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560 0043, Japan
    Proc Natl Acad Sci U S A 104:4315-20. 2007

Detail Information

Publications84

  1. pmc Conformational plasticity of RNA for target recognition as revealed by the 2.15 A crystal structure of a human IgG-aptamer complex
    Yusuke Nomura
    Department of Life and Environmental Sciences, Faculty of Engineering, Chiba Institute of Technology, Narashino shi, Chiba 275 0016, Japan
    Nucleic Acids Res 38:7822-9. 2010
    ....
  2. doi request reprint Structure basis for the regulation of glyceraldehyde-3-phosphate dehydrogenase activity via the intrinsically disordered protein CP12
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Structure 19:1846-54. 2011
    ..An unexpected increase in negative charge potential that emerged upon CP12 binding highlights the biological function of CP12 in the sequential assembly of the supramolecular complex...
  3. pmc Crystal structure of the N-terminal domain of the yeast general corepressor Tup1p and its functional implications
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biol Chem 287:26528-38. 2012
    ..This altered structure explains why the mutant cannot bind Cyc8p. The data presented herein highlight the importance of the architecture of the Tup1p N-terminal domain for self-association...
  4. doi request reprint Crystal structure of rice Rubisco and implications for activation induced by positive effectors NADPH and 6-phosphogluconate
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1, Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 422:75-86. 2012
    ....
  5. pmc Approach for growth of high-quality and large protein crystals
    Hiroyoshi Matsumura
    Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    J Synchrotron Radiat 18:16-9. 2011
    ..Here a novel crystallization method that combines TSSG and the large-scale hanging-drop method is reported. A large and single crystal of lysozyme was obtained by this method...
  6. ncbi request reprint Novel cation-pi interaction revealed by crystal structure of thermoalkalophilic lipase
    Hiroyoshi Matsumura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1, Yamadaoka, Suita, Osaka 565 0871, Japan
    Proteins 70:592-8. 2008
  7. ncbi request reprint Structural, thermodynamic, and mutational analyses of a psychrotrophic RNase HI
    Takashi Tadokoro
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Japan
    Biochemistry 46:7460-8. 2007
    ..coli RNase HI. Site-directed mutagenesis studies suggest that the difference in the number of intramolecular ion pairs partly accounts for the difference in stability between MR-1 and E. coli RNases HI...
  8. doi request reprint Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form
    Yuichi Koga
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
    FEBS J 275:2632-43. 2008
    ..These results suggest that the ion pairs in the alpha16 helix contribute to the stabilization of Tk-GK in a cooperative manner...
  9. ncbi request reprint Structural and mutational analysis of Trypanosoma brucei prostaglandin H2 reductase provides insight into the catalytic mechanism of aldo-ketoreductases
    Kubata Bruno Kilunga
    Department of Molecular Behavioral Biology, Osaka Bioscience Institute, 6 2 4 Furuedai, Suita, Osaka 565 0874, Japan
    J Biol Chem 280:26371-82. 2005
    ..We also show Tyr52 acts as the general acid catalyst for 9,10-PQ reduction, and thus we not only elucidate the catalytic mechanism of a PGH2 reductase but also provide an insight into the catalytic specificity of AKRs...
  10. pmc Structure and function of a hexameric copper-containing nitrite reductase
    Masaki Nojiri
    Department of Chemistry, Graduate School of Science, Osaka University, Osaka 560 0043, Japan
    Proc Natl Acad Sci U S A 104:4315-20. 2007
    ..The discussion of the intermolecular electron transfer process from cytochrome c(550) to the H. denitrificans NIR is based on x-ray crystallographic and kinetic results...
  11. ncbi request reprint Four new crystal structures of Tk-subtilisin in unautoprocessed, autoprocessed and mature forms: insight into structural changes during maturation
    Shun ichi Tanaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka, Japan
    J Mol Biol 372:1055-69. 2007
    ..65 A resolution. This structure is virtually identical with that of the autoprocessed form, indicating that the interaction between the two domains is highly intensive and specific...
  12. doi request reprint Requirement of a unique Ca(2+)-binding loop for folding of Tk-subtilisin from a hyperthermophilic archaeon
    Yuki Takeuchi
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Biochemistry 48:10637-43. 2009
    ..These results suggest that the Ca(2+)-binding loop is required for folding of Tk-subtilisin but does not seriously contribute to the stabilization of Tk-subtilisin in a native structure...
  13. doi request reprint Structural insight into the stereoselective production of PGF2α by Old Yellow Enzyme from Trypanosoma cruzi
    Naoki Okamoto
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada oka, Suita, Japan
    J Biochem 150:563-8. 2011
    ....
  14. doi request reprint Crystal structure of Tk-subtilisin folded without propeptide: requirement of propeptide for acceleration of folding
    Shun ichi Tanaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    FEBS Lett 582:3875-8. 2008
    ..17 and 1.8min(-1) at 30 degrees C in the absence and presence of Tk-propeptide, respectively, indicating that Tk-subtilisin does not require Tk-propeptide for folding but requires it for acceleration of folding...
  15. ncbi request reprint Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms
    Yasushi Kai
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, 565 0871, Osaka, Japan
    Arch Biochem Biophys 414:170-9. 2003
    ..Information derived from these three-dimensional structures, combined with related biochemical studies, has established models for the reaction mechanism and allosteric regulation of this important C-fixing enzyme...
  16. ncbi request reprint Requirement of left-handed glycine residue for high stability of the Tk-subtilisin propeptide as revealed by mutational and crystallographic analyses
    Marian A Pulido
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 374:1359-73. 2007
    ..Stabilization of this fold leads to strong binding of Tk-propeptide to Tk-subtilisin, high resistance of Tk-propeptide to proteolytic degradation, and slow maturation of Pro-Tk-subtilisin...
  17. ncbi request reprint The in silico screening and X-ray structure analysis of the inhibitor complex of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase
    Yasuhide Takashima
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biochem 152:133-8. 2012
    ..Combining part of the inhibitor molecule with moieties of the pyrimidine and ribose rings of OMP and UMP represents a suitable avenue for further development of anti-malarial drugs...
  18. pmc Crystallization and preliminary X-ray analysis of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis
    Haruka Tamura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 65:147-50. 2009
    ..3, b = 91.5, c = 107.0 A, beta = 90.8 degrees. The asymmetric unit contained four molecules of DK-MTP-1P enolase, with a V(M) value of 2.2 A(3) Da(-1) and a solvent content of 43%...
  19. doi request reprint Human hematopoietic prostaglandin D synthase inhibitor complex structures
    Yuji Kado
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871, Japan
    J Biochem 151:447-55. 2012
    ..These factors may contribute to the 50-fold difference in the IC(50) values obtained for the two inhibitors...
  20. doi request reprint Identification of the interactions critical for propeptide-catalyzed folding of Tk-subtilisin
    Shun ichi Tanaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 394:306-19. 2009
    ..We propose that Glu201-mediated interactions are critical for initiation of Tkpro-catalyzed folding of Tk-subtilisin...
  21. pmc Crystal structure of 5-methylthioribose 1-phosphate isomerase product complex from Bacillus subtilis: implications for catalytic mechanism
    Haruka Tamura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Osaka, Japan
    Protein Sci 17:126-35. 2008
    ..The highly conserved residues at the active site, namely, Cys160 and Asp240 are most likely to be involved in catalysis. The structural analysis sheds light on its catalytic mechanism of M1Pi...
  22. ncbi request reprint Crystal structure of unautoprocessed precursor of subtilisin from a hyperthermophilic archaeon: evidence for Ca2+-induced folding
    Shun ichi Tanaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biol Chem 282:8246-55. 2007
    ....
  23. ncbi request reprint Crystal structure and structure-based mutational analyses of RNase HIII from Bacillus stearothermophilus: a new type 2 RNase H with TBP-like substrate-binding domain at the N terminus
    Hyongi Chon
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 356:165-78. 2006
    ....
  24. pmc Crystal structure of TBP-interacting protein (Tk-TIP26) and implications for its inhibition mechanism of the interaction between TBP and TATA-DNA
    Takahiko Yamamoto
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871, Japan
    Protein Sci 15:152-61. 2006
    ....
  25. doi request reprint Structure of the apo decarbamylated form of 2,3-diketo-5-methylthiopentyl-1-phosphate enolase from Bacillus subtilis
    Haruka Tamura
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
    Acta Crystallogr D Biol Crystallogr 65:942-51. 2009
    ..Based on these results, the characteristic structural features of DK-MTP-1P enolase are discussed...
  26. ncbi request reprint Crystal structure of a family I.3 lipase from Pseudomonas sp. MIS38 in a closed conformation
    Clement Angkawidjaja
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    FEBS Lett 581:5060-4. 2007
    ..Lid2 forms a helical hairpin in an open conformation, but does not form it and covers the active site in a closed conformation. Based on these results, we discuss on the lid-opening mechanism...
  27. ncbi request reprint X-ray crystallographic and MD simulation studies on the mechanism of interfacial activation of a family I.3 lipase with two lids
    Clement Angkawidjaja
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 400:82-95. 2010
    ..These results suggest that Ca1 functions as a hook for stabilization of a fully opened conformation of lid1 and for initiation of subsequent opening of lid2...
  28. ncbi request reprint Solution-stirring method improves crystal quality of human triosephosphate isomerase
    Hiroaki Adachi
    SOSHO Project Crystal Design Project, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biosci Bioeng 101:83-6. 2006
    ..8 A. These results clearly show that the solution-stirring method is valuable and useful for protein crystallization because of its effectiveness and simplicity...
  29. pmc Crystallization and preliminary X-ray diffraction analysis of orotate phosphoribosyltransferase from the human malaria parasite Plasmodium falciparum
    Yasuhide Takashima
    Division of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 68:244-6. 2012
    ..15, c = 226.94 Å. X-ray diffraction data were collected to 2.5 Å resolution at 100 K using a synchrotron-radiation source...
  30. ncbi request reprint Structure of amyloid beta fragments in aqueous environments
    Kazufumi Takano
    Department of Material and Life Science, Osaka University, Suita, Japan
    FEBS J 273:150-8. 2006
    ..This study also indicates that this fusion technique is useful for obtaining structural information with atomic resolution for amyloidogenic peptides in aqueous environments...
  31. doi request reprint Destabilization of psychrotrophic RNase HI in a localized fashion as revealed by mutational and X-ray crystallographic analyses
    Muhammad S Rohman
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Japan
    FEBS J 276:603-13. 2009
    ..We propose that So-RNase HI is destabilized when compared with its mesophilic and thermophilic counterparts in a localized fashion by increasing the number of amino acid residues unfavourable for protein stability...
  32. pmc Crystallization and preliminary X-ray diffraction study of thermostable RNase HIII from Bacillus stearothermophilus
    Hyongi Chon
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:293-5. 2005
    ..The crystals belong to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 66.73, b = 108.62, c = 48.29 A. Assuming one molecule per asymmetric unit, the VM value was 2.59 A3 Da(-1) and the solvent content was 52.2%...
  33. pmc Crystallization and preliminary X-ray diffraction studies of an RNA aptamer in complex with the human IgG Fc fragment
    Shigeru Sugiyama
    Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:942-4. 2008
    ..Preliminary X-ray diffraction studies revealed that the crystals belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 83.7, b = 107.2, c = 79.0 A. A data set has been collected to 2.2 A resolution...
  34. ncbi request reprint Substrate-induced closing of the active site revealed by the crystal structure of pantothenate synthetase from Staphylococcus aureus
    Atsuko Satoh
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka, Japan
    Biochemistry 49:6400-10. 2010
    ..Therefore, the complex structure seems to represent a catalytic state poised for in-line nucleophilic attack on PA. These data also offer an alternative strategy for designing novel compounds that selectively inhibit PS activity...
  35. doi request reprint Growth of protein crystals in hydrogels prevents osmotic shock
    Shigeru Sugiyama
    Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    J Am Chem Soc 134:5786-9. 2012
    ..This technique allowed us essentially to increase the mechanical stability of the crystals, preventing serious damage to the crystals caused by osmotic shock. Thus, this method may accelerate structure-based drug discoveries...
  36. ncbi request reprint First determination of the inhibitor complex structure of human hematopoietic prostaglandin D synthase
    Tsuyoshi Inoue
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871
    J Biochem 135:279-83. 2004
    ..14 micro M in the presence of Mg(2+). We have to avoid steric hindrance of the GSH molecule that was stabilized by intracellular Mg(2+) in the mM range in the cytosol for further development of structure-based anti-allergic drugs...
  37. pmc Crystallization and preliminary X-ray diffraction study of an active-site mutant of pro-Tk-subtilisin from a hyperthermophilic archaeon
    Shun ichi Tanaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:902-5. 2006
    ..69, b = 121.78, c = 77.53 A. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V(M) was calculated to be 2.6 A(3) Da(-1) and the solvent content was 53.1%...
  38. ncbi request reprint Structural reorganization of the copper binding site involving Thr15 of mavicyanin from Cucurbita pepo medullosa (zucchini) upon reduction
    Yong Xie
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871
    J Biochem 137:455-61. 2005
    ..2001) J. Inorg. Biochem. 83, 223-227]. The rotation of Thr15 and the hydrogen bonding with the ligand Gln96 may constitute structural evidence of the decrease in the reduction potential at high pH...
  39. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies of dissimilatory nitrite reductase isolated from Hyphomicrobium denitrificans A3151
    Yong Xie
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University 1 2, Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr D Biol Crystallogr 60:2383-6. 2004
    ..X-ray diffraction data were collected to 3.5 A resolution. To solve the crystal structure of HdNIR, the multiwavelength anomalous dispersion (MAD) method and the molecular-replacement method are currently being used...
  40. ncbi request reprint Application of femtosecond laser ablation for detaching grown protein crystals from glass capillary tube
    Masafumi Kashii
    Department of Orthopaedic Surgery, Osaka University Graduate School of Medicine, 2 2 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biosci Bioeng 102:372-4. 2006
    ..X-ray diffraction analysis demonstrated that femtosecond laser irradiation has little effect on crystallinity. This technique will contribute to progress in structural genomics as a powerful tool...
  41. pmc Extracellular overproduction and preliminary crystallographic analysis of a family I.3 lipase
    Clement Angkawidjaja
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:187-9. 2007
    ..79, b = 84.06, c = 87.04 A. Assuming the presence of one molecule per asymmetric unit, the Matthews coefficient V(M) was calculated to be 2.73 A3 Da(-1) and the solvent content was 55%...
  42. ncbi request reprint Processing of membrane protein crystal using ultraviolet laser irradiation
    Hiroshi Kitano
    Department of Electrical Engineering, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biosci Bioeng 100:50-3. 2005
    ..The results described here indicate that PULSA processing is an effective tool for membrane protein crystals, as well as for soluble protein crystals...
  43. ncbi request reprint Protein crystal growth with a two-liquid system and stirring solution
    Hiroaki Adachi
    Department of Electrical Engineering and Venture Business Laboratory, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Synchrotron Radiat 11:121-4. 2004
    ..When compared to conventional techniques, both techniques result in a reduced number of crystals, as well as the growth of large crystals...
  44. ncbi request reprint Identification of single Mn(2+) binding sites required for activation of the mutant proteins of E.coli RNase HI at Glu48 and/or Asp134 by X-ray crystallography
    Yasuo Tsunaka
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Mol Biol 345:1171-83. 2005
    ..The binding position of the first manganese ion is probably forced to shift to site 1 or site 2 upon binding of the second manganese ion...
  45. pmc Overproduction and preliminary crystallographic study of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3
    Hyongi Chon
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:319-22. 2005
    ..75, b = 86.84, c = 137.30 A. Assuming one molecule per asymmetric unit, the VM value was 2.19 A3 Da(-1) and the solvent content was 43.3%...
  46. ncbi request reprint X-ray structure of Galdieria Rubisco complexed with one sulfate ion per active site
    Yousuke Okano
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka, 565 0871, Japan
    FEBS Lett 527:33-6. 2002
    ..This interaction is likely to be crucial to understanding for stabilizing the loop 6 in the closed state and to making a higher affinity for anionic ligands...
  47. pmc Crystallization and preliminary X-ray analysis of methylthioribose-1-phosphate isomerase from Bacillus subtilis
    Haruka Tamura
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:595-8. 2005
    ..2, c = 154.7 A. The asymmetric unit contains two molecules of MtnA, with a VM value of 2.4 A3 Da(-1) and a solvent content of 48%...
  48. ncbi request reprint Solution stirring initiates nucleation and improves the quality of adenosine deaminase crystals
    Hiroaki Adachi
    Department of Electrical Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr D Biol Crystallogr 61:759-62. 2005
    ..The results reported here indicate that the solution-stirring technique promotes nucleation and improves the quality of protein crystals...
  49. pmc Mechanistic insights into the hydrolysis and synthesis of ceramide by neutral ceramidase
    Tsuyoshi Inoue
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871, Japan
    J Biol Chem 284:9566-77. 2009
    ..Furthermore, insights into the actions of PaCD and eukaryotic neutral CDases as an exotoxin and mediators of sphingolipid signaling are also revealed, respectively...
  50. ncbi request reprint Mechanism of metal activation of human hematopoietic prostaglandin D synthase
    Tsuyoshi Inoue
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    Nat Struct Biol 10:291-6. 2003
    ..This effect explains a four-fold reduction in the K(m) of the enzyme for GSH. The structure provides insights into how Ca2+ or Mg2+ binding activates human hematopoietic PGD synthase...
  51. ncbi request reprint Crystal structure of intein homing endonuclease II encoded in DNA polymerase gene from hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1
    Hiroyoshi Matsumura
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
    Proteins 63:711-5. 2006
  52. ncbi request reprint Conformational contagion in a protein: structural properties of a chameleon sequence
    Kazufumi Takano
    Department of Material and Life Science, Osaka University, Suita, Japan
    Proteins 68:617-25. 2007
    ..We propose this "conformational contagion" as a new nonlocal determinant factor in protein structure and misfolding related to protein conformational diseases...
  53. ncbi request reprint Structural basis for the decarboxylation of orotidine 5'-monophosphate (OMP) by Plasmodium falciparum OMP decarboxylase
    Keiji Tokuoka
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    J Biochem 143:69-78. 2008
    ..The structural basis of substrate or product binding to PfOMPDC will help to uncover the decarboxylation mechanism and facilitate structure-based optimization of antimalarial drugs...
  54. pmc Crystallization and preliminary X-ray diffraction study of glycerol kinase from the hyperthermophilic archaeon Thermococcus kodakaraensis
    Ryota Katsumi
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:126-9. 2007
    ..7 A(3) Da(-1) and the solvent content was 54.1%. The protein was also cocrystallized with substrates and diffraction data were collected to 2.7 A resolution...
  55. ncbi request reprint Crystal structure of FtsA from Staphylococcus aureus
    Junso Fujita
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    FEBS Lett 588:1879-85. 2014
    ..We confirmed that SaFtsZ and SaFtsA associate in vitro, and found that SaFtsZ GTPase activity is enhanced by interaction with SaFtsA...
  56. pmc Expression, purification, crystallization and preliminary crystallographic analysis of spermidine acetyltransferase from Escherichia coli
    Mayumi Niiyama
    Graduate School of Science, Osaka University, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 69:884-7. 2013
    ..5 Å resolution and belonged to the cubic space group P23, with unit-cell parameters a = b = c = 148.7 Å. They contained four molecules per asymmetric unit...
  57. ncbi request reprint The significance of the flexible loop in the azurin (Az-iso2) from the obligate methylotroph Methylomonas sp. strain J
    Tsuyoshi Inoue
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita 565 0871, Japan
    J Mol Biol 333:117-24. 2003
    ..We discuss why the electron-transfer activity of Az-iso2 is fivefold higher than that of Az-iso1...
  58. pmc Crystallization and preliminary crystallographic studies of PotA, a membrane-associated ATPase of the spermidine-preferential uptake system in Thermotoga maritima
    Shigeru Sugiyama
    Graduate School of Science, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr F Struct Biol Commun 70:738-41. 2014
    ..9, c = 221.2 Å, α = 90, β = 90, γ = 120°, indicating that a dimer was present in the asymmetric unit. ..
  59. ncbi request reprint Crystal structure of activated ribulose-1,5-bisphosphate carboxylase/oxygenase from green alga Chlamydomonas reinhardtii complexed with 2-carboxyarabinitol-1,5-bisphosphate
    Eiichi Mizohata
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamada oka, Suita, Osaka 565 0871, Japan
    J Mol Biol 316:679-91. 2002
    ..Furthermore, the unusual electron density of residue 471 of the L-subunit, which has been deduced to be threonine from the genomic DNA sequence, suggests that the residue is isoleucine produced by RNA editing or O(gamma)-methylthreonine...
  60. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies of Trypanosoma brucei prostaglandin F(2 alpha) synthase
    Yousuke Okano
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Yamada oka Suita, Osaka 565 0871, Japan
    J Biochem 132:859-61. 2002
    ..The crystal belonged to a tetragonal space group, P4(1)2(1)2 or P4(3)2(1)2, with unit-cell parameters of a = b = 112.3 A, and c = 140.0 A. Native data up to 2.6 A resolution were collected from the crystal using our home facility...
  61. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies of mavicyanin from Cucurbita pepo medullosa
    Yong Xie
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    Acta Crystallogr D Biol Crystallogr 59:1474-6. 2003
    ..X-ray diffraction data were collected to 1.6 A resolution. To solve the structure of mavicyanin, the MAD method as well as a Patterson search method using the structure of stellacyanin as a starting model are presently being utilized...
  62. ncbi request reprint Crystallization and preliminary X-ray analysis of TBP-interacting protein from the hyperthermophilic archaeon Thermococcus kodakaraensis strain KOD1
    Takahiko Yamamoto
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Yamada oka 2 1, Suita, Osaka 565 0871, Japan
    Acta Crystallogr D Biol Crystallogr 59:372-4. 2003
    ..83, c = 86.41 A, and diffract to 2.2 A using synchrotron radiation. MAD data was collected and a Bijvoet difference Patterson map showed strong peaks sufficient to determine the positions of the Se atoms...
  63. ncbi request reprint Crystal structures of C4 form maize and quaternary complex of E. coli phosphoenolpyruvate carboxylases
    Hiroyoshi Matsumura
    Department of Materials Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    Structure 10:1721-30. 2002
    ..On the basis of these molecular structures, the mechanisms for the carboxylation reaction and for the allosteric regulation of PEPC are proposed...
  64. pmc Structure of the inhibitor complex of old yellow enzyme from Trypanosoma cruzi
    Keishi Yamaguchi
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Yamada oka 2 1, Suita, Osaka 565 0871, Japan
    J Synchrotron Radiat 18:66-9. 2011
    ..The binding motif of menadione, known as one of the inhibitors for TcOYE, should accelerate the structure-based development of novel anti-chagasic drugs that inhibit PGF(2α) production specifically...
  65. pmc Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus
    Junso Fujita
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2 1 Yamadaoka, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 69:895-8. 2013
    ..31, b = 102.78, c = 105.90 Å, β = 96.54°. The calculated Matthews coefficient suggested that the asymmetric unit contained three or four monomers...
  66. pmc Crystallization and preliminary X-ray diffraction analysis of mouse prostaglandin F2α synthase, AKR1B3
    Yasuhide Takashima
    Department of Applied Chemistry, Graduate School of Engineering, Osaka University, Suita, Osaka, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:1630-2. 2011
    ..62, c = 120.76 Å. X-ray diffraction data were collected to 2.4 Å resolution at 100 K using a synchrotron-radiation source...
  67. ncbi request reprint Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution
    Hyongi Chon
    Department of Material and Life Science, Graduate School of Engineering, Osaka University, Osaka, Japan
    Proteins 61:685-8. 2005
  68. ncbi request reprint [New progress in crystallization technology of membrane protein and introduction of pharamaceutical innovation value chain]
    Tsuyoshi Inoue
    Graduate School of Engineering Osaka University, Yamada oka, Suita City, Japan
    Yakugaku Zasshi 128:497-505. 2008
    ..In this paper, we report the recent research work on the crystallization of membrane proteins and the development of a method for in silico drug discovery...
  69. pmc Crystallization and preliminary neutron diffraction studies of HIV-1 protease cocrystallized with inhibitor KNI-272
    Hiroyoshi Matsumura
    Graduate School of Engineering, Osaka University, Suita, Osaka 565 0871, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 64:1003-6. 2008
    ..The data set was integrated and scaled to 2.3 A resolution in space group P2(1)2(1)2, with unit-cell parameters a = 59.5, b = 87.4, c = 46.8 A...
  70. pmc Crystallization and preliminary X-ray diffraction analysis of thioredoxin peroxidase from the aerobic hyperthermophilic archaeon Aeropyrum pernix K1
    Tsutomu Nakamura
    National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563 8577, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 61:323-5. 2005
    ..2, b = 126.3, c = 213.7 A, alpha = 80.4, beta = 80.3, gamma = 70.7 degrees. Calculation of the self-rotation function showed that the protein quaternary structure includes a fivefold axis and five twofold axes...
  71. pmc Crystallization and preliminary X-ray analysis of the tRNA thiolation enzyme MnmA from Escherichia coli complexed with tRNA(Glu)
    Tomoyuki Numata
    Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta cho, Midori ku, Yokohama shi, Kanagawa 226 8501, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:368-71. 2006
    ..5, b = 108.0, c = 211.2 A and a = 238.1, b = 102.1, c = 108.2 angstroms, beta = 117.0 degrees, respectively. The asymmetric units of these crystals are expected to contain two, one and two MnmA-tRNA(Glu) complexes, respectively...
  72. ncbi request reprint Crystal structure of thioredoxin peroxidase from aerobic hyperthermophilic archaeon Aeropyrum pernix K1
    Tsutomu Nakamura
    National Institute of Advanced Industrial Science and Technology AIST, Ikeda, Osaka, Japan
    Proteins 62:822-6. 2006
  73. ncbi request reprint Structural basis of compound recognition by adenosine deaminase
    Takayoshi Kinoshita
    Exploratory Research Laboratories, Fujisawa Pharmaceutical Company, Ltd, 5 2 3, Tokodai, Tsukuba, Ibaraki 300 2698, Japan
    Biochemistry 44:10562-9. 2005
    ..On the other hand, while occupied, the overall conformation remains in the open form. This structural understanding should greatly assist structure-oriented drug design and enable control of the enzymatic activity...
  74. ncbi request reprint Structural mechanism for coordination of proofreading and polymerase activities in archaeal DNA polymerases
    Toshihiro Kuroita
    Tsuruga Institute of Biotechnology, Toyobo Co, Ltd, 10 24 Toyo Cho, Tsuruga, Fukui 914 0047, Japan
    J Mol Biol 351:291-8. 2005
    ..Our data suggest that electrostatic and hydrophobic interactions between the unique loop of the exonuclease domain and the tip of the Thumb domain are essential for determining the properties of these DNA polymerases...
  75. ncbi request reprint Phosphoenolpyruvate carboxylase: a new era of structural biology
    Katsura Izui
    Laboratory of Plant Physiology, Graduate School of Biostudies, Kyoto University, Kyoto 606 8502, Japan
    Annu Rev Plant Biol 55:69-84. 2004
    ..We present the reaction mechanism of PEPC in which we assign the roles of individual amino acid residues. We discuss the unique molecular property of PEPC kinase and its possible regulation at the post-translational level...
  76. ncbi request reprint The crystal structure of the outer membrane protein VceC from the bacterial pathogen Vibrio cholerae at 1.8 A resolution
    Luca Federici
    Department of Biochemistry, University of Cambridge, United Kingdom
    J Biol Chem 280:15307-14. 2005
    ..Our analyses of the external surfaces of VceC and other channel proteins suggest that different classes of efflux pumps have distinct architectures. We discuss the implications of these findings for mechanisms of drug and protein export...
  77. doi request reprint Maize C4-form phosphoenolpyruvate carboxylase engineered to be functional in C3 plants: mutations for diminished sensitivity to feedback inhibitors and for increased substrate affinity
    Tatsuya Endo
    Laboratory of Plant Physiology, Faculty of Agriculture, Kyoto University, Kitashirakawa, Sakyo ku, Kyoto 606 8502, Japan
    J Exp Bot 59:1811-8. 2008
    ..5)(PEP) with equal maximal catalytic activity (V(m)) to the wild-type PEPC, which will be quite useful as a component of the C(4)-like pathway to be introduced into C(3) plants...
  78. ncbi request reprint Maize phosphoenolpyruvate carboxylase. Mutations at the putative binding site for glucose 6-phosphate caused desensitization and abolished responsiveness to regulatory phosphorylation
    Akiko Takahashi-Terada
    Graduate School of Biostudies, Kyoto University, Kitashirakawa, Sakyo ku, Kyoto 606 8502, Japan
    J Biol Chem 280:11798-806. 2005
    ..An apparent lack of kinetic competition between the phosphate groups of Glc-6-P and of phospho-Ser at 15 suggested the distinctness of their binding sites. The possible roles of these Arg residues are discussed...
  79. ncbi request reprint Enzymatic characterization of 5-methylthioribose 1-phosphate isomerase from Bacillus subtilis
    Yohtaro Saito
    Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara, Japan
    Biosci Biotechnol Biochem 71:2021-8. 2007
    ..7 kJ mol(-1). The enzyme, with a molecular mass of 76 kDa, was composed of two subunits. The equilibrium constant in the reversible isomerase reaction [MTRu-1-P]/[MTR-1-P] was 6. We discuss the possible reaction mechanism...
  80. pmc Oxidation of archaeal peroxiredoxin involves a hypervalent sulfur intermediate
    Tsutomu Nakamura
    National Institute of Advanced Industrial Science and Technology, Ikeda, Osaka 563 8577, Japan
    Proc Natl Acad Sci U S A 105:6238-42. 2008
    ..This study provides evidence that a hypervalent sulfur compound occupies an important position in biochemical processes...
  81. ncbi request reprint A novel mechanism of allosteric regulation of archaeal phosphoenolpyruvate carboxylase: a combined approach to structure-based alignment and model assessment
    Hiroyoshi Matsumura
    Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
    Protein Eng Des Sel 19:409-19. 2006
    ..Our novel observations will help design more efficient molecules for ecological and industrial use...
  82. pmc Crystallization and preliminary crystallographic analysis of orotidine 5'-monophosphate decarboxylase from the human malaria parasite Plasmodium falciparum
    Sudaratana R Krungkrai
    Unit of Biochemistry, Department of Medical Science, Faculty of Science, Rangsit University, Patumthani 12000, Thailand
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:542-5. 2006
    ..The crystal exhibits trigonal symmetry (space group R3), with hexagonal unit-cell parameters a = b = 201.81, c = 44.03 A. With a dimer in the asymmetric unit, the solvent content is 46% (V(M) = 2.3 A3 Da(-1))...
  83. pmc Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus
    Tomoya Tsukazaki
    Institute for Virus Research, Kyoto University, Kyoto 606 8507, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:376-80. 2006
    ..These results provide information that is essential for the determination of the three-dimensional structure of this important membrane component of the protein-translocation machinery...
  84. pmc Preparation, crystallization and preliminary crystallographic analysis of old yellow enzyme from Trypanosoma cruzi
    Shigeru Sugiyama
    Maruwa Foods Co Ltd, Tsutsui cho 170 1, Yamatokoriyama, Nara 639 1123, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 63:896-8. 2007
    ..The crystals were suitable for X-ray crystallographic studies and diffracted to 1.70 A resolution. A Patterson search method is in progress using the structure of OYE from Pseudomonas putida as a starting model...