Nobutada Tanaka

Summary

Affiliation: Showa University
Country: Japan

Publications

  1. ncbi request reprint Crystal structures of mouse autocrine motility factor in complex with carbohydrate phosphate inhibitors provide insight into structure-activity relationship of the inhibitors
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Shinagawa ku, Tokyo, Japan
    J Mol Biol 356:312-24. 2006
  2. pmc Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms
    Masaru Tsunoda
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Nucleic Acids Res 35:4289-300. 2007
  3. ncbi request reprint [Structural biology for developing antimalarial compounds]
    Nobutada Tanaka
    School of Pharmacy, Showa University
    Yakugaku Zasshi 133:527-37. 2013
  4. ncbi request reprint [Structural and functional studies on proteins as potential drug discovery targets]
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Yakugaku Zasshi 127:1673-83. 2007
  5. ncbi request reprint Crystallization of the N-terminal ankyrin repeat domain of the 2-5A-dependent endoribonuclease, RNase L
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Tokyo, Japan
    Protein Pept Lett 12:387-9. 2005
  6. ncbi request reprint Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    J Mol Biol 343:1007-17. 2004
  7. pmc Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Hatanodai, Shinagawa ku, Tokyo, Japan
    EMBO J 23:3929-38. 2004
  8. doi request reprint Molecular basis for peroxisomal localization of tetrameric carbonyl reductase
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Structure 16:388-97. 2008
  9. ncbi request reprint Crystal structure of glutathione-independent formaldehyde dehydrogenase
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, 142 8555, Tokyo, Japan
    Chem Biol Interact 143:211-8. 2003
  10. ncbi request reprint Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, 142 8555, Tokyo, Japan
    J Mol Biol 324:519-33. 2002

Collaborators

Detail Information

Publications42

  1. ncbi request reprint Crystal structures of mouse autocrine motility factor in complex with carbohydrate phosphate inhibitors provide insight into structure-activity relationship of the inhibitors
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Shinagawa ku, Tokyo, Japan
    J Mol Biol 356:312-24. 2006
    ..The present structure-activity relationship studies will be valuable not only for designing more effective AMF inhibitors but also for studying general protein-inhibitor interactions...
  2. pmc Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms
    Masaru Tsunoda
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Nucleic Acids Res 35:4289-300. 2007
    ..On the other hand, the recognition mode of Tyr-AMP is conserved among the TyrRSs from the three kingdoms...
  3. ncbi request reprint [Structural biology for developing antimalarial compounds]
    Nobutada Tanaka
    School of Pharmacy, Showa University
    Yakugaku Zasshi 133:527-37. 2013
    ..falciparum. We expect that the structure-function relationship studies on Plasmodium proteins are useful for developing the more effective antimalarial compounds...
  4. ncbi request reprint [Structural and functional studies on proteins as potential drug discovery targets]
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Yakugaku Zasshi 127:1673-83. 2007
    ....
  5. ncbi request reprint Crystallization of the N-terminal ankyrin repeat domain of the 2-5A-dependent endoribonuclease, RNase L
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Tokyo, Japan
    Protein Pept Lett 12:387-9. 2005
    ..03 Angstroms, and c = 82.64 Angstroms. There is one molecule per asymmetric unit. The crystals diffract to at least 2.1 Angstroms resolution using synchrotron radiation and are suitable for X-ray structure analysis at high resolution...
  6. ncbi request reprint Crystal structure of S-adenosyl-L-homocysteine hydrolase from the human malaria parasite Plasmodium falciparum
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    J Mol Biol 343:1007-17. 2004
    ..A replacement of Cys59 by Thr results in mutant PfSAHH, which shows HsSAHH-like nucleoside inhibitor sensitivity. The present structure should provide opportunities to design potent and selective PfSAHH inhibitors...
  7. pmc Structural basis for recognition of 2',5'-linked oligoadenylates by human ribonuclease L
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Hatanodai, Shinagawa ku, Tokyo, Japan
    EMBO J 23:3929-38. 2004
    ..Interestingly, two structurally equivalent 2-5A binding motifs are found at repeats 2 and 4. The structural basis for 2-5A recognition by ANK is essential for designing stable 2-5As with a high likelihood of activating RNase L...
  8. doi request reprint Molecular basis for peroxisomal localization of tetrameric carbonyl reductase
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Structure 16:388-97. 2008
    ..These findings indicate that the PTS1 receptor Pex5p in the cytosol recognizes the monomeric form of PerCR whose C-terminal PTS1 is exposed, and that this PerCR is targeted into the peroxisome, thereby forming a tetramer...
  9. ncbi request reprint Crystal structure of glutathione-independent formaldehyde dehydrogenase
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, 142 8555, Tokyo, Japan
    Chem Biol Interact 143:211-8. 2003
    ....
  10. ncbi request reprint Crystal structure of formaldehyde dehydrogenase from Pseudomonas putida: the structural origin of the tightly bound cofactor in nicotinoprotein dehydrogenases
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, 142 8555, Tokyo, Japan
    J Mol Biol 324:519-33. 2002
    ....
  11. ncbi request reprint Crystal structure of the catalytic fragment of human brain 2',3'-cyclic-nucleotide 3'-phosphodiesterase
    Yasumitsu Sakamoto
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    J Mol Biol 346:789-800. 2005
    ..Since the overall structure of hCNP-CF differs considerably from that of RNase A, it is likely that the similar active sites with two catalytic histidine residues in these enzymes arose through convergent evolution...
  12. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies of mouse autocrine motility factor
    Noriko Naba
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr D Biol Crystallogr 60:2084-6. 2004
    ..Complexes with four-, five- and six-carbon carbohydrate phosphate inhibitors have also been crystallized. The crystals diffract to at least 1.8 A resolution and are suitable for X-ray structure analyses at high resolution...
  13. ncbi request reprint Crystallization and preliminary X-ray crystallographic analysis of yeast tyrosyl-tRNA synthetase complexed with its cognate tRNA
    Yoshio Kusakabe
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Protein Pept Lett 13:417-9. 2006
    ..85 Angstrom, and c = 330.3 Angstrom. The asymmetric unit contains one molecule each of yTyrRS and tRNA(Tyr) (one-half of a 2:2 complex). X-ray diffraction data have been collected up to 2.5 Angstrom resolution...
  14. ncbi request reprint Three-dimensional structure of the ternary complex of yeast tyrosyl-tRNA synthetase
    Masaru Tsunoda
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Nucleic Acids Symp Ser (Oxf) . 2004
    ..Here we report the crystal structure of yeast Tyrosyl-tRNA synthetase (yTyrRS) complexed with its cognate tRNA(Tyr) and Tyr-AMP analog...
  15. pmc Molecular basis of fosmidomycin's action on the human malaria parasite Plasmodium falciparum
    Tomonobu Umeda
    School of Pharmacy, Showa University, Tokyo 142 8555, Japan
    Sci Rep 1:9. 2011
    ..We expect the present structures to be useful guides for the design of more effective antimalarial compounds...
  16. ncbi request reprint Inhibition mechanism of cytokine activity of human autocrine motility factor examined by crystal structure analyses and site-directed mutagenesis studies
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    J Mol Biol 318:985-97. 2002
    ..Since the E4P is one of the smallest compounds having AMF inhibitor activity, knowledge of the present crystal structure would provide an insight into the lead compound design of more effective AMF inhibitors...
  17. pmc Crystallization and preliminary X-ray crystallographic study of 1-deoxy-D-xylulose 5-phosphate reductoisomerase from Plasmodium falciparum
    Tomonobu Umeda
    School of Pharmacy, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:330-2. 2010
    ..85 A resolution were collected from a monoclinic crystal form belonging to space group C2 with unit-cell parameters a = 168.89, b = 59.65, c = 86.58 A, beta = 117.8 degrees. Structural analysis by molecular replacement is in progress...
  18. pmc Crystallization and preliminary X-ray crystallographic analysis of human autotaxin
    Keigo Inoue
    School of Pharmacy, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 67:450-3. 2011
    ..X-ray diffraction data were collected to 3.0 Å resolution from a monoclinic crystal form belonging to space group C2, with unit-cell parameters a = 311.4, b = 147.9, c = 176.9 Å, β = 122.6°...
  19. ncbi request reprint Crystallization and preliminary X-ray crystallographic analysis of Plasmodium falciparum S-adenosyl-L-homocysteine hydrolase
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Protein Pept Lett 11:201-5. 2004
    ..There are four subunits (one tetramer) per asymmetric unit. X-ray diffraction data have been collected up to 2.8 A resolution. Self-rotation function studies suggest that the tetrameric PfSAHH molecule has the 222 point group symmetry...
  20. pmc Crystallization and preliminary X-ray crystallographic study of phosphoglucose isomerase from Plasmodium falciparum
    Ken ichi Aoki
    School of Pharmacy, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:333-6. 2010
    ..5 A resolution were collected from an orthorhombic crystal form belonging to space group P2(1)2(1)2(1) with unit-cell parameters a = 103.3, b = 104.1, c = 114.6 A. Structural analysis by molecular replacement is in progress...
  21. pmc Crystallization and preliminary X-ray crystallographic studies of pig heart carbonyl reductase
    Ken ichi Aoki
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 62:1037-40. 2006
    ..Form II crystals belong to the tetragonal space group P4(1)2(1)2, with unit-cell parameters a = b = 120.10, c = 147.00 A, and diffract to 2.2 A resolution. Both crystal forms are suitable for X-ray structure analysis at high resolution...
  22. ncbi request reprint Three-dimensional structure of S-adenosyl-L-homocysteine hydrolase from Plasmodium falciparum
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Nucleic Acids Symp Ser (Oxf) . 2004
    ..Here we report the crystal structure of PfSAHH. The present structure should provide opportunities to design potent and selective PfSAHH inhibitors...
  23. pmc Structural insights into the reaction mechanism of S-adenosyl-L-homocysteine hydrolase
    Yoshio Kusakabe
    School of Pharmacy, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Sci Rep 5:16641. 2015
    ..The presence of the water molecule is consistent with the reaction mechanism proposed by Palmer &Abeles in 1979. These results provide insights into the reaction mechanism of the SAHH enzyme. ..
  24. pmc Crystallization and preliminary X-ray crystallographic studies of dipeptidyl peptidase 11 from Porphyromonas gingivalis
    Yasumitsu Sakamoto
    School of Pharmacy, Iwate Medical University, 2 1 1 Nishitokuta, Yahaba, Iwate 028 3694, Japan
    Acta Crystallogr F Struct Biol Commun 71:206-10. 2015
    ..33, b = 103.60, c = 177.33 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress...
  25. pmc Crystallization of mouse S-adenosyl-L-homocysteine hydrolase
    Masaaki Ishihara
    School of Pharmacy, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:313-5. 2010
    ..55 A resolution were collected from an orthorhombic crystal form belonging to space group I222 with unit-cell parameters a = 100.64, b = 104.44, c = 177.31 A. Structural analysis by molecular replacement is in progress...
  26. pmc Crystallization and preliminary X-ray crystallographic studies of dipeptidyl aminopeptidase BII from Pseudoxanthomonas mexicana WO24
    Yasumitsu Sakamoto
    School of Pharmacy, Iwate Medical University, 2 1 1 Nishitokuta, Yahaba, Iwate 028 3694, Japan
    Acta Crystallogr F Struct Biol Commun 70:221-4. 2014
    ..55, b = 130.86, c = 170.87 Å. Structural analysis by the multi-wavelength anomalous diffraction method is in progress...
  27. ncbi request reprint Molecular basis for recognition of 2',5'-linked oligoadenylates by the N-terminal ankyrin repeat domain of human ribonuclease L
    Nobutada Tanaka
    School of Pharmaceutical Sciences, Showa University, 1 5 8 Hatanodai, Shinagawa ku, Tokyo 142 8555, Japan
    Nucleic Acids Symp Ser (Oxf) . 2005
    ..Two structurally equivalent 2-5A binding motifs are found at repeats 2 and 4. The molecular basis for 2-5A recognition by RNase L is essential for designing stable 2-5As with a high likelihood of activating RNase L...
  28. ncbi request reprint Three-dimensional structure of a cyclic-nucleotide phosphodiesterase from human brain
    Yasumitsu Sakamoto
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Nucleic Acids Symp Ser (Oxf) . 2004
    ..Recently, CNP has been identified as a member of the 2H phosphoesterase superfamily. Here we have determined the crystal structure of the catalytic fragment of human CNP (hCNP-CF) at 1.3 A resolution...
  29. pmc Structural and mutational analyses of dipeptidyl peptidase 11 from Porphyromonas gingivalis reveal the molecular basis for strict substrate specificity
    Yasumitsu Sakamoto
    School of Pharmacy, Iwate Medical University, 2 1 1 Nishitokuta, Yahaba, Iwate 028 3694, Japan
    Sci Rep 5:11151. 2015
    ..In addition, the present structure analyses could be useful templates for the design of specific inhibitors of DPP11s from pathogenic organisms. ..
  30. pmc Crystallization and preliminary X-ray crystallographic studies of an exo-beta-D-glucosaminidase from Trichoderma reesei
    Yasumitsu Sakamoto
    School of Pharmacy, Iwate Medical University, 2 1 1 Nishitokuta, Yahaba, Iwate 028 3694, Japan
    Acta Crystallogr Sect F Struct Biol Cryst Commun 66:309-12. 2010
    ..84, b = 81.62, c = 183.14 A, and diffracted to 2.4 A resolution. Both crystal forms were suitable for X-ray structure analysis at high resolution...
  31. ncbi request reprint Structural comparison analysis of 2H phosphodiesterase family proteins
    Yasumitsu Sakamoto
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Nucleic Acids Symp Ser (Oxf) . 2007
    ..Here we report the structure-function relationship studies of two hydrophobic residues in CNP family proteins...
  32. ncbi request reprint Crystallization and preliminary X-ray crystallographic studies of human 2',3'-cyclic nucleotide 3'-phosphodiesterase
    Yasumitsu Sakamoto
    School of Pharmaceutical Sciences, Showa University, Tokyo 142 8555, Japan
    Acta Crystallogr D Biol Crystallogr 60:2095-7. 2004
    ..39, b = 55.35, c = 78.76 A. There is one molecule per asymmetric unit. The crystals diffract to at least 1.8 A resolution using synchrotron radiation and are suitable for X-ray structure analysis at high resolution...
  33. ncbi request reprint Preliminary crystallographic studies of the creatinine amidohydrolase from Pseudomonas putida
    Kiyoshi Ito
    Biotechnology, Graduate School of Biomedical Sciences, Nagasaki University, 1 14 Bunkyo machi, Nagasaki 852 8521, Japan
    Acta Crystallogr D Biol Crystallogr 58:2180-1. 2002
    ..0, b = 150.7, c = 167.1 A. Native data were collected to 1.8 A resolution by a rotation method at 100 K using an ADSC Quantum 4R CCD detector with synchrotron radiation...
  34. ncbi request reprint The enzymatic activity of phosphoglucose isomerase is not required for its cytokine function
    Soichi Tsutsumi
    Karmanos Cancer Institute, Wayne State University School of Medicine, 110 East Warren, Detroit, MI 48201, USA
    FEBS Lett 534:49-53. 2003
    ..The results demonstrate that the enzymatic activity of PGI is not essential for either receptor binding or cytokine function of human PGI...
  35. ncbi request reprint Crystal structures of creatininase reveal the substrate binding site and provide an insight into the catalytic mechanism
    Tadashi Yoshimoto
    Graduate School of Biomedical Sciences, Nagasaki University, 1 14 Bunkyo machi, Nagasaki 852 8521, Japan
    J Mol Biol 337:399-416. 2004
    ..We propose a new two-step catalytic mechanism possibly common to creatininases in which the Wat1 acts as the attacking nucleophile in the water-adding step and the Wat2 acts as the catalytic acid in the ring-opening step...
  36. ncbi request reprint Functional characterization of 2',5'-linked oligoadenylate binding determinant of human RNase L
    Masayuki Nakanishi
    Department of Biomolecular Science, Faculty of Engineering, Gifu University, Yanagido 1 1, Gifu 501 1193, Japan
    J Biol Chem 280:41694-9. 2005
    ..It was also found that the crystal structure of the ankyrin repeat domain L.2-5A complex accurately portrays the 2-5A binding mode in full-length RNase L...
  37. ncbi request reprint Novel inhibitor for prolyl aminopeptidase from Serratia marcescens and studies on the mechanism of substrate recognition of the enzyme using the inhibitor
    Takahiko Inoue
    Graduate School of Biomedical Sciences, Nagasaki University, 1 14 Bunkyo machi, Nagasaki 852 8521, Japan
    Arch Biochem Biophys 416:147-54. 2003
    ....
  38. ncbi request reprint The autocrine motility factor (AMF) and AMF-receptor combination needs sugar chain recognition ability and interaction using the C-terminal region of AMF
    Arayo Haga
    Gifu Pharmaceutical University, 5 6 1 Mitahora Higashi, Gifu 502 8585, Japan
    J Mol Biol 358:741-53. 2006
    ..These results suggest that the N-glyco side-chain of AMFR is a trigger and that interaction between the 117-C-terminal part of AMF and the extracellular core protein of AMFR is needed during AMF-AMFR interactions...
  39. ncbi request reprint Differential regulation of phosphoglucose isomerase/autocrine motility factor activities by protein kinase CK2 phosphorylation
    Takashi Yanagawa
    Tumor Progression and Metastasis Program, Karmanos Cancer Institute, 110 E Warren Ave, Detroit, Michigan 48201, USA
    J Biol Chem 280:10419-26. 2005
    ..The process by which phosphorylation modulates the enzymatic activity of PGI thus has an important implication for the understanding of the biological regulation of this key glucose metabolism-regulating enzyme...
  40. ncbi request reprint Mutational analyses of Plasmodium falciparum and human S-adenosylhomocysteine hydrolases
    Masayuki Nakanishi
    Department of Biomolecular Science, Faculty of Engineering, Gifu University, 1 1 Yanagido, Gifu 501 1193, Japan
    Mol Biochem Parasitol 143:146-51. 2005
    ..These results showed that steric hindrance between a functional group at the 2-position of an adenine nucleoside inhibitor and Thr60 of the human enzyme, not an electrostatic effect, contributed to inhibitor selectivity...
  41. doi request reprint Characterization of human DHRS4: an inducible short-chain dehydrogenase/reductase enzyme with 3beta-hydroxysteroid dehydrogenase activity
    Toshiyuki Matsunaga
    Laboratory of Biochemistry, Gifu Pharmaceutical University, 5 6 1 Mitahora Higashi, Gifu 502 8585, Japan
    Arch Biochem Biophys 477:339-47. 2008
    ..The results suggest a novel mechanism of cold inactivation and role of the inducible human DHRS4 in 3beta-hydroxysteroid synthesis and xenobiotic carbonyl metabolism...
  42. doi request reprint Scalable purification and characterization of the extracellular domain of human autotaxin from prokaryotic cells
    Arayo Haga
    Research Institute for Health and Environmental Science, Gifu Prefectural Government, 1 1, Naka Fudougaoka, Kakamigahara 504 0838, Japan
    Protein Expr Purif 59:9-17. 2008
    ..This is a first report for scalable purification of the ATX molecule and the rhATX S48 should be a good tool for immunization of anti-ATX or crystallographic analysis of ATX...