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Volumn 320, Issue 3, 2004, Pages 979-991

Molecular models for shikimate pathway enzymes of Xylella fastidiosa

Author keywords

Drug design; Shikimate pathway; Structural bioinformatics; Xylella fastidiosa

Indexed keywords

3 DEHYDROQUINATE DEHYDRATASE; 3 DEHYDROQUINATE SYNTHASE; 3 DEOXY DEXTRO ARABINOHEPTULOSONATE 7 PHOSPHATE SYNTHASE; 5 ENOLPYROXYLSHIKIMATE 3 PHOSPHATE SYNTHASE; BACTERIAL ENZYME; CHORISMATE SYNTHASE; ENZYME INHIBITOR; ISOENZYME; SHIKIMATE DEHYDROGENASE; SHIKIMATE KINASE; SHIKIMIC ACID; UNCLASSIFIED DRUG;

EID: 3042791901     PISSN: 0006291X     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bbrc.2004.05.220     Document Type: Article
Times cited : (27)

References (56)
  • 1
    • 0034644159 scopus 로고    scopus 로고
    • The genome sequence of the plant pathogen Xylella fastidiosa
    • Simpson A.J.G., et al. The genome sequence of the plant pathogen Xylella fastidiosa. Nature. 406:2000;151-157
    • (2000) Nature , vol.406 , pp. 151-157
    • Simpson, A.J.G.1
  • 2
    • 0034644191 scopus 로고    scopus 로고
    • The bugs from Brazil
    • Bevan M. The bugs from Brazil. Nature. 406:2000;140-141
    • (2000) Nature , vol.406 , pp. 140-141
    • Bevan, M.1
  • 6
    • 0034951945 scopus 로고    scopus 로고
    • A metabolic node in action: Chorismate-utilizing enzymes in microrganisms
    • Dosselaere F., Vanderleyden J. A metabolic node in action: chorismate-utilizing enzymes in microrganisms. Crit. Rev. Microbiol. 27(2):2001;75-131
    • (2001) Crit. Rev. Microbiol. , vol.27 , Issue.2 , pp. 75-131
    • Dosselaere, F.1    Vanderleyden, J.2
  • 7
    • 0029104066 scopus 로고
    • The shikimate pathway as an entry to aromatic secondary metabolism
    • Herrmann K.M. The shikimate pathway as an entry to aromatic secondary metabolism. Plant Physiol. 107:1995;7-12
    • (1995) Plant Physiol. , vol.107 , pp. 7-12
    • Herrmann, K.M.1
  • 8
    • 0029768873 scopus 로고    scopus 로고
    • Prediction of the three-dimensional structure of human interleukin-7 by homology modeling
    • Kroemer R.T., Doughty S.W., Robinson A.J., Richards W.G. Prediction of the three-dimensional structure of human interleukin-7 by homology modeling. Protein Eng. 9(6):1996;493-498
    • (1996) Protein Eng. , vol.9 , Issue.6 , pp. 493-498
    • Kroemer, R.T.1    Doughty, S.W.2    Robinson, A.J.3    Richards, W.G.4
  • 9
    • 0023305986 scopus 로고
    • Knowledge-based prediction of protein structures and the design of novel molecules
    • Blundell T.L., Sibanda B.L., Sternberg M.J., Thornton J.M. Knowledge-based prediction of protein structures and the design of novel molecules. Nature. 326(6111):1987;347-352
    • (1987) Nature , vol.326 , Issue.6111 , pp. 347-352
    • Blundell, T.L.1    Sibanda, B.L.2    Sternberg, M.J.3    Thornton, J.M.4
  • 11
    • 0027136282 scopus 로고
    • Comparative protein modelling by satisfaction of spatial restraints
    • Sali A., Blundell T.L. Comparative protein modelling by satisfaction of spatial restraints. J. Mol. Biol. 234:1993;779-815
    • (1993) J. Mol. Biol. , vol.234 , pp. 779-815
    • Sali, A.1    Blundell, T.L.2
  • 12
    • 0028051828 scopus 로고
    • Derivation of rules for comparative protein modeling from a database of protein structure alignments
    • Sali A., Overington J.P. Derivation of rules for comparative protein modeling from a database of protein structure alignments. Protein Sci. 3(9):1994;1582-1596
    • (1994) Protein Sci. , vol.3 , Issue.9 , pp. 1582-1596
    • Sali, A.1    Overington, J.P.2
  • 13
    • 0028871814 scopus 로고
    • Evaluation of comparative protein modeling by MODELLER
    • Sali A., Potterton L., Yuan F., van Vlijmen H., Karplus M. Evaluation of comparative protein modeling by MODELLER. Proteins. 23(3):1995;318-326
    • (1995) Proteins , vol.23 , Issue.3 , pp. 318-326
    • Sali, A.1    Potterton, L.2    Yuan, F.3    Van Vlijmen, H.4    Karplus, M.5
  • 14
    • 0028991962 scopus 로고
    • Modeling mutations and homologous proteins
    • Sali A. Modeling mutations and homologous proteins. Curr. Opin. Biotechnol. 6(4):1995;437-451
    • (1995) Curr. Opin. Biotechnol. , vol.6 , Issue.4 , pp. 437-451
    • Sali, A.1
  • 16
    • 0022336792 scopus 로고
    • Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm
    • Braun W., Go N. Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm. J. Mol. Biol. 186(3):1985;611-626
    • (1985) J. Mol. Biol. , vol.186 , Issue.3 , pp. 611-626
    • Braun, W.1    Go, N.2
  • 18
    • 0028103275 scopus 로고
    • The CCP4 suite: Programs for proteins crystallography
    • Collaborative Computational Project No. 4, The CCP4 suite: programs for proteins crystallography, Acta Crystallogr. D 50 (1994) 760-763
    • (1994) Acta Crystallogr. D , vol.50 , pp. 760-763
  • 21
    • 0025830469 scopus 로고
    • A method to identify protein sequences that fold into a known three-dimensional structure
    • Bowie J.U., Luthy R., Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science. 253:1991;164-170
    • (1991) Science , vol.253 , pp. 164-170
    • Bowie, J.U.1    Luthy, R.2    Eisenberg, D.3
  • 22
    • 0026610767 scopus 로고
    • Assessment of protein models with three-dimensional profiles
    • Luthy R., Bowie J., Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature. 356:1992;83-85
    • (1992) Nature , vol.356 , pp. 83-85
    • Luthy, R.1    Bowie, J.2    Eisenberg, D.3
  • 23
    • 0020997912 scopus 로고
    • Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
    • Kabsch W., Sander C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers. 22(12):1983;2577-2637
    • (1983) Biopolymers , vol.22 , Issue.12 , pp. 2577-2637
    • Kabsch, W.1    Sander, C.2
  • 25
    • 0028857259 scopus 로고
    • The shikimate pathway: Early steps in the biosynthesis of aromatic compounds
    • Herrmann K.A. The shikimate pathway: early steps in the biosynthesis of aromatic compounds. Plant Cell. 7:1995;907-919
    • (1995) Plant Cell , vol.7 , pp. 907-919
    • Herrmann, K.A.1
  • 26
    • 0032537722 scopus 로고    scopus 로고
    • Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis
    • Carpenter E.P., Hawkins A.R., Frost J.W., Brown K.A. Structure of dehydroquinate synthase reveals an active site capable of multistep catalysis. Nature. 394(6690):1998;299-302
    • (1998) Nature , vol.394 , Issue.6690 , pp. 299-302
    • Carpenter, E.P.1    Hawkins, A.R.2    Frost, J.W.3    Brown, K.A.4
  • 27
    • 0016345760 scopus 로고
    • Chemical and biological evolution of a nucleotide binding protein
    • Rossmann M.G., Moras D., Olsen K.W. Chemical and biological evolution of a nucleotide binding protein. Nature. 250:1974;194-199
    • (1974) Nature , vol.250 , pp. 194-199
    • Rossmann, M.G.1    Moras, D.2    Olsen, K.W.3
  • 28
    • 0029562477 scopus 로고
    • NAD-binding domains of dehydrogenases
    • Lesk A.M. NAD-binding domains of dehydrogenases. Curr. Opin. Struct. Biol. 5:1995;775-783
    • (1995) Curr. Opin. Struct. Biol. , vol.5 , pp. 775-783
    • Lesk, A.M.1
  • 29
    • 0038820015 scopus 로고    scopus 로고
    • The 2.3 Å crystal of the shikimate 5-deydrogenase orthologue YdiB from E. coli suggests a novel catalytic enviroment for an NAD-dependent dehydrogenase
    • Benach J., Lee I., Edstrom W., Kuzin A.P., Chiang Y., Actons T.B., Monteliones G.T., Hunt J.F. The 2.3. Å crystal of the shikimate 5-deydrogenase orthologue YdiB from E. coli suggests a novel catalytic enviroment for an NAD-dependent dehydrogenase J. Biol. Chem. 278:2003;19176-19182
    • (2003) J. Biol. Chem , vol.278 , pp. 19176-19182
    • Benach, J.1    Lee, I.2    Edstrom, W.3    Kuzin, A.P.4    Chiang, Y.5    Actons, T.B.6    Monteliones, G.T.7    Hunt, J.F.8
  • 31
    • 0028961335 scopus 로고
    • SCOP: A structural classification of proteins database for the investigation of sequences and structures
    • Murzin A.G., Brenner S.E., Hubbard T., Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247:1995;536-540
    • (1995) J. Mol. Biol. , vol.247 , pp. 536-540
    • Murzin, A.G.1    Brenner, S.E.2    Hubbard, T.3    Chothia, C.4
  • 32
    • 0038265866 scopus 로고    scopus 로고
    • Structures of Shikimate dehydrogenase AroE and its paralog YdiB - A common structural framework for different activities
    • Michel G., Roszak A.W., Sauvé V., Maclean J., Matte A., Coggins J.R., Cygler M., Lapthorn A.J. Structures of Shikimate dehydrogenase AroE and its paralog YdiB - a common structural framework for different activities. J. Biol. Chem. 278(21):2003;19463-19472
    • (2003) J. Biol. Chem. , vol.278 , Issue.21 , pp. 19463-19472
    • Michel, G.1    Roszak, A.W.2    Sauvé, V.3    MacLean, J.4    Matte, A.5    Coggins, J.R.6    Cygler, M.7    Lapthorn, A.J.8
  • 33
    • 0042131870 scopus 로고    scopus 로고
    • Shikimate dehydrogenase structure reveals novel fold
    • Vogan E. Shikimate dehydrogenase structure reveals novel fold. Structure. 11:2003;902-903
    • (2003) Structure , vol.11 , pp. 902-903
    • Vogan, E.1
  • 34
    • 12944300317 scopus 로고
    • Binding of nucleotides by proteins
    • Schulz G.E. Binding of nucleotides by proteins. Curr. Opin. Struct. Biol. 2:1992;61-67
    • (1992) Curr. Opin. Struct. Biol. , vol.2 , pp. 61-67
    • Schulz, G.E.1
  • 35
    • 0028579433 scopus 로고
    • Protein structural similarities predicted by a sequence-structure compatibility method
    • Matsuo Y., Nishikawa K. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci. 3(11):1994;2055-2063
    • (1994) Protein Sci. , vol.3 , Issue.11 , pp. 2055-2063
    • Matsuo, Y.1    Nishikawa, K.2
  • 36
    • 0029644168 scopus 로고    scopus 로고
    • Adenylate kinase motions during catalysis: An energetic counterweight balancing substrate binding
    • Müller C.W., Schlauderer G.J., Reinstein J., Schulz G.E. Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding. Structure. 4:1996;147-156
    • (1996) Structure , vol.4 , pp. 147-156
    • Müller, C.W.1    Schlauderer, G.J.2    Reinstein, J.3    Schulz, G.E.4
  • 37
    • 0027528934 scopus 로고
    • Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers
    • Gerstein M., Schulz G., Chothia C. Domain closure in adenylate kinase. Joints on either side of two helices close like neighboring fingers. J. Mol. Biol. 229(2):1993;494-501
    • (1993) J. Mol. Biol. , vol.229 , Issue.2 , pp. 494-501
    • Gerstein, M.1    Schulz, G.2    Chothia, C.3
  • 38
    • 0036300993 scopus 로고    scopus 로고
    • Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis
    • Gu Y., Reshetnikova L., Li Y., Wu Y., Yan H., Singh S., Ji X. Crystal structure of shikimate kinase from Mycobacterium tuberculosis reveals the dynamic role of the LID domain in catalysis. J. Mol. Biol. 319(3):2002;779-789
    • (2002) J. Mol. Biol. , vol.319 , Issue.3 , pp. 779-789
    • Gu, Y.1    Reshetnikova, L.2    Li, Y.3    Wu, Y.4    Yan, H.5    Singh, S.6    Ji, X.7
  • 40
    • 0032557708 scopus 로고    scopus 로고
    • The three-dimensional structure of shikimate kinase
    • Krell T., Coggins J.R., Lapthorn A.J The three-dimensional structure of shikimate kinase. J. Mol. Biol. 178(5):1998;983-997
    • (1998) J. Mol. Biol. , vol.178 , Issue.5 , pp. 983-997
    • Krell, T.1    Coggins, J.R.2    Lapthorn, A.J.3
  • 41
    • 0029864204 scopus 로고    scopus 로고
    • Structural constraints on the ternary complex of 5-enolpyruvyl shikimate 3-phosphate synthase from rotational-echo double resonance NMR
    • McDowell L.M., Schmidt A., Cohen E.R., Studelska D.R., Schaefer J. Structural constraints on the ternary complex of 5-enolpyruvyl shikimate 3-phosphate synthase from rotational-echo double resonance NMR. J. Mol. Biol. 256:1996;160-171
    • (1996) J. Mol. Biol. , vol.256 , pp. 160-171
    • McDowell, L.M.1    Schmidt, A.2    Cohen, E.R.3    Studelska, D.R.4    Schaefer, J.5
  • 42
    • 0029053555 scopus 로고
    • Reevaluating glyphosate as a transition state inhibitor of EPSP synthase: Identification of an EPSP synthase-EPSP-glyphosate ternary complex
    • Sammons R.D., Gruys K.J., Anderson K.S., Johnson K.A., Sikorski J.A. Reevaluating glyphosate as a transition state inhibitor of EPSP synthase: identification of an EPSP synthase-EPSP-glyphosate ternary complex. Biochemistry. 34:1995;6433-6440
    • (1995) Biochemistry , vol.34 , pp. 6433-6440
    • Sammons, R.D.1    Gruys, K.J.2    Anderson, K.S.3    Johnson, K.A.4    Sikorski, J.A.5
  • 43
    • 0029868793 scopus 로고
    • Ligand geometry of the ternary complex of 5-enolpyruvyl shikimate 3-phosphate synthase from rotational-echo double-resonance NMR
    • McDowell L.M, Klug C.A., Beusen D.D., Schaefer J. Ligand geometry of the ternary complex of 5-enolpyruvyl shikimate 3-phosphate synthase from rotational-echo double-resonance NMR. Biochemistry. 35:1995;5395-5403
    • (1995) Biochemistry , vol.35 , pp. 5395-5403
    • McDowell, L.M.1    Klug, C.A.2    Beusen, D.D.3    Schaefer, J.4
  • 44
    • 0036833740 scopus 로고    scopus 로고
    • How the mutation glycine96 to alanine confers glyphosate insensitivity to 5-enolpyruvyl shikimate-3-phosphate synthase from Escherichia coli
    • Eschenburg S., Healy M.L., Priestman M.A., Lushington G.H., Schönbrunn E. How the mutation glycine96 to alanine confers glyphosate insensitivity to 5-enolpyruvyl shikimate-3-phosphate synthase from Escherichia coli. Planta. 216:2002;129-135
    • (2002) Planta , vol.216 , pp. 129-135
    • Eschenburg, S.1    Healy, M.L.2    Priestman, M.A.3    Lushington, G.H.4    Schönbrunn, E.5
  • 47
    • 0348047617 scopus 로고    scopus 로고
    • Crystal structure of chorismate synthase from Auifex aeolicus reveals a novel beta alpha beta sandwich topology
    • Viola C.M., Saridakis V., Christendat D. Crystal structure of chorismate synthase from Auifex aeolicus reveals a novel beta alpha beta sandwich topology. Proteins. 54:2004;166-169
    • (2004) Proteins , vol.54 , pp. 166-169
    • Viola, C.M.1    Saridakis, V.2    Christendat, D.3
  • 48
    • 0032944057 scopus 로고    scopus 로고
    • A unique reaction in a common pathway: Mechanism and function of chorismate synthase in the shikimate pathway
    • Macheroux P., Schmid J., Amrhein N., Schaller A. A unique reaction in a common pathway: mechanism and function of chorismate synthase in the shikimate pathway. Planta. 207:1999;325-334
    • (1999) Planta , vol.207 , pp. 325-334
    • MacHeroux, P.1    Schmid, J.2    Amrhein, N.3    Schaller, A.4
  • 49
    • 0344868502 scopus 로고    scopus 로고
    • The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction
    • Maclean J., Ali S. The structure of chorismate synthase reveals a novel flavin binding site fundamental to a unique chemical reaction. Structure. 11:2003;1499-1511
    • (2003) Structure , vol.11 , pp. 1499-1511
    • MacLean, J.1    Ali, S.2
  • 53
    • 0026319199 scopus 로고
    • Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons
    • Nicholls A., Sharp K.A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 11(4):1991;281-296
    • (1991) Proteins , vol.11 , Issue.4 , pp. 281-296
    • Nicholls, A.1    Sharp, K.A.2    Honig, B.3
  • 54
    • 0027968068 scopus 로고
    • CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice
    • Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680
    • (1994) Nucleic Acids Res. , vol.22 , pp. 4673-4680
    • Thompson, J.D.1    Higgins, D.G.2    Gibson, T.J.3
  • 55
    • 0026244229 scopus 로고
    • MOLSCRIPT: A program to produce both detailed and schematic plots of proteins
    • Kraulis P.J. MOLSCRIPT: a program to produce both detailed and schematic plots of proteins. J. Appl. Crystallogr. 24:1991;946-950
    • (1991) J. Appl. Crystallogr. , vol.24 , pp. 946-950
    • Kraulis, P.J.1
  • 56
    • 0030815133 scopus 로고    scopus 로고
    • Raster3D: Photorealistic molecular graphics
    • Merritt E.A., Bacon D.J. Raster3D: photorealistic molecular graphics. Methods Enzymol. 277:1997;505-524
    • (1997) Methods Enzymol. , vol.277 , pp. 505-524
    • Merritt, E.A.1    Bacon, D.J.2


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