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Volumn 388, Issue 5, 2009, Pages 1009-1021

Insights Into the Enzymatic Mechanism of 6-Phosphogluconolactonase from Trypanosoma brucei Using Structural Data and Molecular Dynamics Simulation

Author keywords

6 phosphogluconolactonase; crystal structure; enzymatic mechanism; molecular dynamics simulation; Trypanosoma brucei

Indexed keywords

6 PHOSPHOGLUCONOLACTONASE; PENTOSE PHOSPHATE; PROTOZOAL PROTEIN; UNCLASSIFIED DRUG;

EID: 67349251957     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2009.03.063     Document Type: Article
Times cited : (18)

References (31)
  • 1
    • 0023464501 scopus 로고
    • Compartmentation of carbohydrate metabolism in trypanosomes
    • Opperdoes F. Compartmentation of carbohydrate metabolism in trypanosomes. Annu. Rev. Microbiol. 41 (1987) 127-151
    • (1987) Annu. Rev. Microbiol. , vol.41 , pp. 127-151
    • Opperdoes, F.1
  • 4
    • 43049092997 scopus 로고    scopus 로고
    • Design, synthesis and trypanocidal activity of lead compounds based on inhibitors of parasite glycolysis
    • Nowicki M.W., Tulloch L.B., Worrall L., McNae I.W., Hannaert V., Michels P.A., et al. Design, synthesis and trypanocidal activity of lead compounds based on inhibitors of parasite glycolysis. Bioorg. Med. Chem. 16 (2008) 5050-5061
    • (2008) Bioorg. Med. Chem. , vol.16 , pp. 5050-5061
    • Nowicki, M.W.1    Tulloch, L.B.2    Worrall, L.3    McNae, I.W.4    Hannaert, V.5    Michels, P.A.6
  • 5
    • 0035860710 scopus 로고    scopus 로고
    • NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase
    • Miclet E., Stoven V., Michels P.A., Opperdoes F.R., Lallemand J.Y., and Duffieux F. NMR spectroscopic analysis of the first two steps of the pentose-phosphate pathway elucidates the role of 6-phosphogluconolactonase. J. Biol. Chem. 276 (2001) 34840-34846
    • (2001) J. Biol. Chem. , vol.276 , pp. 34840-34846
    • Miclet, E.1    Stoven, V.2    Michels, P.A.3    Opperdoes, F.R.4    Lallemand, J.Y.5    Duffieux, F.6
  • 6
    • 33846817140 scopus 로고    scopus 로고
    • Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei
    • Delarue M., Duclert-Savatier N., Miclet E., Haouz A., Giganti D., Ouazzani J., et al. Three dimensional structure and implications for the catalytic mechanism of 6-phosphogluconolactonase from Trypanosoma brucei. J. Mol. Biol. 366 (2007) 868-881
    • (2007) J. Mol. Biol. , vol.366 , pp. 868-881
    • Delarue, M.1    Duclert-Savatier, N.2    Miclet, E.3    Haouz, A.4    Giganti, D.5    Ouazzani, J.6
  • 8
    • 0034811498 scopus 로고    scopus 로고
    • Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA
    • Wang J., Morin P., Wang W., and Kollman P.A. Use of MM-PBSA in reproducing the binding free energies to HIV-1 RT of TIBO derivatives and predicting the binding mode to HIV-1 RT of efavirenz by docking and MM-PBSA. J. Am. Chem. Soc. 123 (2001) 5221-5230
    • (2001) J. Am. Chem. Soc. , vol.123 , pp. 5221-5230
    • Wang, J.1    Morin, P.2    Wang, W.3    Kollman, P.A.4
  • 9
    • 0029646095 scopus 로고
    • Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution
    • Oliva G., Fontes M.R., Garratt R.C., Altamirano M.M., Calcagno M.L., and Horjales E. Structure and catalytic mechanism of glucosamine 6-phosphate deaminase from Escherichia coli at 2.1 Å resolution. Structure 3 (1995) 1323-1332
    • (1995) Structure , vol.3 , pp. 1323-1332
    • Oliva, G.1    Fontes, M.R.2    Garratt, R.C.3    Altamirano, M.M.4    Calcagno, M.L.5    Horjales, E.6
  • 10
    • 0032853037 scopus 로고    scopus 로고
    • Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway
    • Collard F., Collet J.F., Gerin I., Veiga-da-Cunha M., and Van Schaftingen E. Identification of the cDNA encoding human 6-phosphogluconolactonase, the enzyme catalyzing the second step of the pentose phosphate pathway. FEBS Lett. 459 (1999) 223-226
    • (1999) FEBS Lett. , vol.459 , pp. 223-226
    • Collard, F.1    Collet, J.F.2    Gerin, I.3    Veiga-da-Cunha, M.4    Van Schaftingen, E.5
  • 11
    • 21244505806 scopus 로고    scopus 로고
    • Structure and kinetics of a monomeric glucosamine 6-phosphate deaminase: missing link of the NagB superfamily?
    • Vincent F., Davies G.J., and Brannigan J.A. Structure and kinetics of a monomeric glucosamine 6-phosphate deaminase: missing link of the NagB superfamily?. J. Biol. Chem. 280 (2005) 19649-19655
    • (2005) J. Biol. Chem. , vol.280 , pp. 19649-19655
    • Vincent, F.1    Davies, G.J.2    Brannigan, J.A.3
  • 12
    • 14844334902 scopus 로고    scopus 로고
    • Competitive inhibitors of Mycobacterium tuberculosis ribose-5-phosphate isomerase B reveal new information about the reaction mechanism
    • Roos A.K., Burgos E., Ericsson D.J., Salmon L., and Mowbray S.L. Competitive inhibitors of Mycobacterium tuberculosis ribose-5-phosphate isomerase B reveal new information about the reaction mechanism. J. Biol. Chem. 280 (2005) 6416-6422
    • (2005) J. Biol. Chem. , vol.280 , pp. 6416-6422
    • Roos, A.K.1    Burgos, E.2    Ericsson, D.J.3    Salmon, L.4    Mowbray, S.L.5
  • 13
    • 0027879008 scopus 로고
    • Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants
    • Kabsch W. Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Crystallogr. 26 (1993) 795-800
    • (1993) J. Appl. Crystallogr. , vol.26 , pp. 795-800
    • Kabsch, W.1
  • 14
    • 37349121133 scopus 로고    scopus 로고
    • Model preparation in MOLREP and examples of model improvement using X-ray data
    • Lebedev A.A., Vagin A.A., and Murshudov G.N. Model preparation in MOLREP and examples of model improvement using X-ray data. Acta. Crystallogr. D 64 (2008) 33-39
    • (2008) Acta. Crystallogr. D , vol.64 , pp. 33-39
    • Lebedev, A.A.1    Vagin, A.A.2    Murshudov, G.N.3
  • 15
    • 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 Crystallogr. D 53 (1997) 240-255
    • (1997) Acta Crystallogr. D , vol.53 , pp. 240-255
    • Murshudov, G.N.1    Vagin, A.A.2    Dodson, E.J.3
  • 16
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley P., and Cowtan K. Coot: Model-building tools for molecular graphics. Acta Crystallogr. D 60 (2004) 2126-2132
    • (2004) Acta Crystallogr. D , vol.60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 17
    • 0032922193 scopus 로고    scopus 로고
    • SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model
    • Vaguine A.A., Richelle J., and Wodak S.J. SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model. Acta Crystallogr. D 55 (1999) 191-205
    • (1999) Acta Crystallogr. D , vol.55 , pp. 191-205
    • Vaguine, A.A.1    Richelle, J.2    Wodak, S.J.3
  • 19
  • 21
    • 0001398008 scopus 로고    scopus 로고
    • How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?
    • Wang J., Cieplak P., and Kollman P.A. How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules?. J. Comput. Chem. 21 (2000) 1049-1074
    • (2000) J. Comput. Chem. , vol.21 , pp. 1049-1074
    • Wang, J.1    Cieplak, P.2    Kollman, P.A.3
  • 23
    • 33846823909 scopus 로고
    • Particle mesh Ewald-an Nlog(N) method for Ewald sums in large systems
    • Darden T., York D., and Pedersen L. Particle mesh Ewald-an Nlog(N) method for Ewald sums in large systems. J. Chem. Phys. 98 (1993) 10089-10092
    • (1993) J. Chem. Phys. , vol.98 , pp. 10089-10092
    • Darden, T.1    York, D.2    Pedersen, L.3
  • 25
    • 0031334264 scopus 로고    scopus 로고
    • Adventures in improving the scaling and accuracy of a parallel molecular dynamics program
    • Crowley M.F., Darden T.A., Cheatham III T.E., and Deerfield II D.W. Adventures in improving the scaling and accuracy of a parallel molecular dynamics program. J. Supercomput. 11 (1997) 255-278
    • (1997) J. Supercomput. , vol.11 , pp. 255-278
    • Crowley, M.F.1    Darden, T.A.2    Cheatham III, T.E.3    Deerfield II, D.W.4
  • 27
    • 84946450438 scopus 로고    scopus 로고
    • Algorithms for macromolecular dynamics and constraint dynamics
    • van Gunsteren W.F., and Berendsen H.J.C. Algorithms for macromolecular dynamics and constraint dynamics. Mol. Phys. 34 (1997) 1311-1327
    • (1997) Mol. Phys. , vol.34 , pp. 1311-1327
    • van Gunsteren, W.F.1    Berendsen, H.J.C.2
  • 28
    • 33646940952 scopus 로고
    • Numerical integration of cartesian equations of motion of a system with constrained molecular dynamics of N-alkanes
    • Ryckaert J.P., Ciccotti G., and Berendsen H.J.C. Numerical integration of cartesian equations of motion of a system with constrained molecular dynamics of N-alkanes. J. Comput. Phys. 23 (1977) 327-341
    • (1977) J. Comput. Phys. , vol.23 , pp. 327-341
    • Ryckaert, J.P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 31
    • 33748538349 scopus 로고    scopus 로고
    • Antechamber, an accessory software package for molecular mechanics calculations
    • Wang J., Wang W., Kollman P.A., and Case D.A. Antechamber, an accessory software package for molecular mechanics calculations. J. Mol. Graph. Model. 25 (2006) 247-260
    • (2006) J. Mol. Graph. Model. , vol.25 , pp. 247-260
    • Wang, J.1    Wang, W.2    Kollman, P.A.3    Case, D.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.