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Volumn 366, Issue 4, 2007, Pages 1294-1304

Crystal Structure of d-Erythronate-4-phosphate Dehydrogenase Complexed with NAD

Author keywords

crystal structure; erythronate 4 phosphate dehydrogenase; pdxB; Pseudomonas aeruginosa; pyridoxal 5 phosphate

Indexed keywords

DEXTRO ERYTHRONATE 4 PHOSPHATE DEHYDROGENASE; NICOTINAMIDE ADENINE DINUCLEOTIDE; NUCLEOTIDE BINDING PROTEIN; OXIDOREDUCTASE; PHOSPHATE; TARTARIC ACID; UNCLASSIFIED DRUG;

EID: 33846644014     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2006.12.038     Document Type: Article
Times cited : (14)

References (33)
  • 1
    • 3943113663 scopus 로고    scopus 로고
    • Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations
    • Eliot A.C., and Kirsch J.F. Pyridoxal phosphate enzymes: mechanistic, structural, and evolutionary considerations. Annu. Rev. Biochem. 73 (2004) 383-415
    • (2004) Annu. Rev. Biochem. , vol.73 , pp. 383-415
    • Eliot, A.C.1    Kirsch, J.F.2
  • 2
    • 12344334763 scopus 로고    scopus 로고
    • Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes
    • Tanaka T., Tateno Y., and Gojobori T. Evolution of vitamin B6 (pyridoxine) metabolism by gain and loss of genes. Mol. Biol. Evol. 22 (2005) 243-250
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 243-250
    • Tanaka, T.1    Tateno, Y.2    Gojobori, T.3
  • 4
    • 14044255850 scopus 로고    scopus 로고
    • Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasite Plasmodium falciparum
    • Wrenger C., Eschbach M.L., Muller I.B., Warnecke D., and Walter R.D. Analysis of the vitamin B6 biosynthesis pathway in the human malaria parasite Plasmodium falciparum. J. Biol. Chem. 280 (2005) 5242-5248
    • (2005) J. Biol. Chem. , vol.280 , pp. 5242-5248
    • Wrenger, C.1    Eschbach, M.L.2    Muller, I.B.3    Warnecke, D.4    Walter, R.D.5
  • 5
    • 1542509428 scopus 로고    scopus 로고
    • Biosynthesis of vitamin B6: direct identification of the product of the PdxA-catalyzed oxidation of 4-hydroxy-l-threonine-4-phosphate using electrospray ionization mass spectrometry
    • Banks J., and Cane D.E. Biosynthesis of vitamin B6: direct identification of the product of the PdxA-catalyzed oxidation of 4-hydroxy-l-threonine-4-phosphate using electrospray ionization mass spectrometry. Bioorg. Med. Chem. Letters 14 (2004) 1633-1636
    • (2004) Bioorg. Med. Chem. Letters , vol.14 , pp. 1633-1636
    • Banks, J.1    Cane, D.E.2
  • 6
    • 0031830655 scopus 로고    scopus 로고
    • Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5′-phosphate biosynthesis in Escherichia coli K-12
    • Yang Y., Zhao G., Man T.K., and Winkler M.E. Identification and function of the pdxY gene, which encodes a novel pyridoxal kinase involved in the salvage pathway of pyridoxal 5′-phosphate biosynthesis in Escherichia coli K-12. J. Bacteriol. 180 (1998) 4294-4299
    • (1998) J. Bacteriol. , vol.180 , pp. 4294-4299
    • Yang, Y.1    Zhao, G.2    Man, T.K.3    Winkler, M.E.4
  • 7
    • 1242341226 scopus 로고    scopus 로고
    • Pyridoxine 5′-phosphate synthase: de novo synthesis of vitamin B6 and beyond
    • Garrido-Franco M. Pyridoxine 5′-phosphate synthase: de novo synthesis of vitamin B6 and beyond. Biochim. Biophys. Acta 1647 (2003) 92-97
    • (2003) Biochim. Biophys. Acta , vol.1647 , pp. 92-97
    • Garrido-Franco, M.1
  • 8
    • 0024835757 scopus 로고
    • A new family of 2-hydroxyacid dehydrogenases
    • Grant G.A. A new family of 2-hydroxyacid dehydrogenases. Biochem. Biophys. Res. Commun. 165 (1989) 1371-1374
    • (1989) Biochem. Biophys. Res. Commun. , vol.165 , pp. 1371-1374
    • Grant, G.A.1
  • 9
    • 33646467967 scopus 로고    scopus 로고
    • Overexpression, crystallization and preliminary X-ray crystallographic analysis of erythronate-4-phosphate dehydrogenase from Pseudomonas aeruginosa
    • Ha J.Y., Lee J.H., Kim K.H., Kim D.J., Lee H.H., Kim H.K., et al. Overexpression, crystallization and preliminary X-ray crystallographic analysis of erythronate-4-phosphate dehydrogenase from Pseudomonas aeruginosa. Acta Crystallog. sect. F 62 (2006) 139-141
    • (2006) Acta Crystallog. sect. F , vol.62 , pp. 139-141
    • Ha, J.Y.1    Lee, J.H.2    Kim, K.H.3    Kim, D.J.4    Lee, H.H.5    Kim, H.K.6
  • 10
    • 0028951187 scopus 로고
    • The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase
    • Schuller D.J., Grant G.A., and Banaszak L.J. The allosteric ligand site in the Vmax-type cooperative enzyme phosphoglycerate dehydrogenase. Nature Struct. Biol. 2 (1995) 69-76
    • (1995) Nature Struct. Biol. , vol.2 , pp. 69-76
    • Schuller, D.J.1    Grant, G.A.2    Banaszak, L.J.3
  • 11
    • 17644385239 scopus 로고    scopus 로고
    • Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits
    • Dey S., Grant G.A., and Sacchettini J.C. Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits. J. Biol. Chem. 280 (2005) 14892-14899
    • (2005) J. Biol. Chem. , vol.280 , pp. 14892-14899
    • Dey, S.1    Grant, G.A.2    Sacchettini, J.C.3
  • 14
    • 0028278602 scopus 로고
    • Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 Å resolution
    • Goldberg J.D., Yoshida T., and Brick P. Crystal structure of a NAD-dependent D-glycerate dehydrogenase at 2.4 Å resolution. J. Mol. Biol. 236 (1994) 1123-1140
    • (1994) J. Mol. Biol. , vol.236 , pp. 1123-1140
    • Goldberg, J.D.1    Yoshida, T.2    Brick, P.3
  • 15
    • 0015834475 scopus 로고
    • Comparison of super-secondary structures in proteins
    • Rao S.T., and Rossmann M.G. Comparison of super-secondary structures in proteins. J. Mol. Biol. 76 (1973) 241-256
    • (1973) J. Mol. Biol. , vol.76 , pp. 241-256
    • Rao, S.T.1    Rossmann, M.G.2
  • 16
    • 0027440362 scopus 로고
    • Protein structure comparison by alignment of distance matrices
    • Holm L., and Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233 (1993) 123-138
    • (1993) J. Mol. Biol. , vol.233 , pp. 123-138
    • Holm, L.1    Sander, C.2
  • 19
    • 0001890332 scopus 로고
    • Crystal structure, coenzyme conformations and protein interactions
    • Dolphin D.N.Y. (Ed), Wiley, New York
    • Eklund H., and Bränden C.I. Crystal structure, coenzyme conformations and protein interactions. In: Dolphin D.N.Y. (Ed). Pyridine Nucleotide Coenzymes (1987), Wiley, New York 51-98
    • (1987) Pyridine Nucleotide Coenzymes , pp. 51-98
    • Eklund, H.1    Bränden, C.I.2
  • 20
    • 0027937347 scopus 로고
    • +-dependent formate dehydrogenase
    • +-dependent formate dehydrogenase. Biochem. J. 301 (1994) 625-643
    • (1994) Biochem. J. , vol.301 , pp. 625-643
    • Popov, V.O.1    Lamzin, V.S.2
  • 21
    • 0037435776 scopus 로고    scopus 로고
    • Crystal structures of Tritrichomonas foetus inosine monophosphate dehydrogenase in complex with substrate, cofactor and analogs: a structural basis for the random-in ordered-out kinetic mechanism
    • Prosise G.L., and Luecke H. Crystal structures of Tritrichomonas foetus inosine monophosphate dehydrogenase in complex with substrate, cofactor and analogs: a structural basis for the random-in ordered-out kinetic mechanism. J. Mol. Biol. 326 (2003) 517-527
    • (2003) J. Mol. Biol. , vol.326 , pp. 517-527
    • Prosise, G.L.1    Luecke, H.2
  • 22
    • 0002277561 scopus 로고
    • Structural interactions with enzymes
    • Everse J., Anderson B., and You K. (Eds), Academic Press, New York
    • Grau U.M. Structural interactions with enzymes. In: Everse J., Anderson B., and You K. (Eds). The Pyridine Nucleotide Coenzymes (1982), Academic Press, New York 135-187
    • (1982) The Pyridine Nucleotide Coenzymes , pp. 135-187
    • Grau, U.M.1
  • 23
    • 0028904688 scopus 로고
    • D175 discriminates between NADH and NADPH in the coenzyme binding site of Lactobacillus delbrueckii subsp. bulgaricus D-lactate dehydrogenase
    • Bernard N., Johnsen K., Holbrook J.J., and Delcour J. D175 discriminates between NADH and NADPH in the coenzyme binding site of Lactobacillus delbrueckii subsp. bulgaricus D-lactate dehydrogenase. Biochem. Biophys. Res. Commun. 208 (1995) 895-900
    • (1995) Biochem. Biophys. Res. Commun. , vol.208 , pp. 895-900
    • Bernard, N.1    Johnsen, K.2    Holbrook, J.J.3    Delcour, J.4
  • 24
    • 0021099009 scopus 로고
    • The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase
    • Birktoft L.J., and Banaszak L.J. The presence of a histidine-aspartic acid pair in the active site of 2-hydroxyacid dehydrogenases. X-ray refinement of cytoplasmic malate dehydrogenase. J. Biol. Chem. 258 (1983) 472-482
    • (1983) J. Biol. Chem. , vol.258 , pp. 472-482
    • Birktoft, L.J.1    Banaszak, L.J.2
  • 25
    • 0017324044 scopus 로고    scopus 로고
    • Serine proteases: structure and mechanism of catalysis
    • Kraut J. Serine proteases: structure and mechanism of catalysis. Annu. Rev. Biochem. 46 (1997) 331-358
    • (1997) Annu. Rev. Biochem. , vol.46 , pp. 331-358
    • Kraut, J.1
  • 26
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
    • (1997) Methods Enzymol. , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 28
    • 0037237545 scopus 로고    scopus 로고
    • Automated main-chain model building by template matching and iterative fragment extension
    • Terwilliger T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallog. sect. D 59 (2003) 38-44
    • (2003) Acta Crystallog. sect. D , vol.59 , pp. 38-44
    • Terwilliger, T.C.1
  • 29
    • 84889120137 scopus 로고
    • Improved methods for building protein models in electron density maps and the location of errors in these models
    • Jones T.A., Zou J.Y., Cowan S.W., and Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
    • (1991) Acta Crystallog. sect. A , vol.47 , pp. 110-119
    • Jones, T.A.1    Zou, J.Y.2    Cowan, S.W.3    Kjeldgaard, M.4
  • 30
    • 0030924992 scopus 로고    scopus 로고
    • Refinement of macromolecular structures by the maximum-likelihood method
    • Murshudov G.N., Vagin A.A., and Dodson E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallog. sect. D 53 (1997) 240-255
    • (1997) Acta Crystallog. sect. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 31
    • 0026597444 scopus 로고
    • Free R value: a novel statistical quantity for assessing the accuracy of crystal structures
    • Brünger A.T. Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472-474
    • (1992) Nature , vol.355 , pp. 472-474
    • Brünger, A.T.1
  • 32
    • 0000243829 scopus 로고
    • PROCHECK: a program to check the stereochemical quality of protein structures
    • Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
    • (1993) J. Appl. Crystallog. , vol.26 , pp. 283-291
    • Laskowski, R.A.1    MacArthur, M.W.2    Moss, D.S.3    Thornton, J.M.4
  • 33
    • 0031574072 scopus 로고    scopus 로고
    • The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl. Acids Res. 25 (1997) 4876-4882
    • (1997) Nucl. Acids Res. , vol.25 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5


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