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Volumn 105, Issue 37, 2008, Pages 13829-13834

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

Author keywords

Enzyme dynamics; Phosphoenolpyruvate carboxykinase; Population shift

Indexed keywords

ENZYME; PHOSPHOENOLPYRUVATE CARBOXYKINASE (GTP);

EID: 52949089027     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0805364105     Document Type: Article
Times cited : (135)

References (53)
  • 1
    • 0001858251 scopus 로고
    • Application of a theory of enzyme specificity to protein synthesis
    • Koshland DE (1958) Application of a theory of enzyme specificity to protein synthesis. Proc Natl Acad Sci USA 44:98-104.
    • (1958) Proc Natl Acad Sci USA , vol.44 , pp. 98-104
    • Koshland, D.E.1
  • 2
    • 0001289724 scopus 로고
    • The influence of configuration on enzyme activity. (Translated from German)
    • Fisher E (1894) The influence of configuration on enzyme activity. (Translated from German). Dtsch Chem Ges 27:2984-2993.
    • (1894) Dtsch Chem Ges , vol.27 , pp. 2984-2993
    • Fisher, E.1
  • 3
    • 33748614305 scopus 로고    scopus 로고
    • Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis
    • Antoniou D, Basner J, Nunez S, Schwartz SD (2006) Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis. Chem Rev 106:3170-3187.
    • (2006) Chem Rev , vol.106 , pp. 3170-3187
    • Antoniou, D.1    Basner, J.2    Nunez, S.3    Schwartz, S.D.4
  • 4
    • 33748619206 scopus 로고    scopus 로고
    • An NMR perspective on enzyme dynamics
    • Boehr DD, Dyson HJ, Wright PE (2006) An NMR perspective on enzyme dynamics. Chem Rev 106:3055-3079.
    • (2006) Chem Rev , vol.106 , pp. 3055-3079
    • Boehr, D.D.1    Dyson, H.J.2    Wright, P.E.3
  • 6
    • 33748633480 scopus 로고    scopus 로고
    • Electrostatic basis for enzyme catalysis
    • Warshel A, et al. (2006) Electrostatic basis for enzyme catalysis. Chem Rev 106:3210-3235.
    • (2006) Chem Rev , vol.106 , pp. 3210-3235
    • Warshel, A.1
  • 7
    • 0032966864 scopus 로고    scopus 로고
    • Antigen recognition by conformational selection
    • Berger C, et al. (1999) Antigen recognition by conformational selection. FEBS Lett 450:149-153.
    • (1999) FEBS Lett , vol.450 , pp. 149-153
    • Berger, C.1
  • 8
    • 0035432947 scopus 로고    scopus 로고
    • Molecular recognition by induced fit: How fit is the concept?
    • Bosshard HR (2001) Molecular recognition by induced fit: How fit is the concept? News Physiol Sci 16:171-173.
    • (2001) News Physiol Sci , vol.16 , pp. 171-173
    • Bosshard, H.R.1
  • 9
    • 0027943261 scopus 로고
    • Conformational isomerism and the diversity of antibodies
    • Foote J, Milstein C (1994) Conformational isomerism and the diversity of antibodies. Proc Natl Acad Sci USA 91:10370-10374.
    • (1994) Proc Natl Acad Sci USA , vol.91 , pp. 10370-10374
    • Foote, J.1    Milstein, C.2
  • 10
    • 0033970020 scopus 로고    scopus 로고
    • Folding and binding cascades: Dynamic landscapes and population shifts
    • Kumar S, Ma B, Tsai CJ, Sinha N, Nussinov R (2000) Folding and binding cascades: Dynamic landscapes and population shifts. Protein Sci 9:10-19.
    • (2000) Protein Sci , vol.9 , pp. 10-19
    • Kumar, S.1    Ma, B.2    Tsai, C.J.3    Sinha, N.4    Nussinov, R.5
  • 11
    • 0029561993 scopus 로고
    • Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition
    • Leder L, et al. (1995) Spectroscopic, calorimetric, and kinetic demonstration of conformational adaptation in peptide-antibody recognition. Biochemistry 34:16509-16518.
    • (1995) Biochemistry , vol.34 , pp. 16509-16518
    • Leder, L.1
  • 12
    • 0036147568 scopus 로고    scopus 로고
    • Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations
    • Ma B, Shatsky M, Wolfson HJ, Nussinov R (2002) Multiple diverse ligands binding at a single protein site: A matter of pre-existing populations. Protein Sci 11:184-197.
    • (2002) Protein Sci , vol.11 , pp. 184-197
    • Ma, B.1    Shatsky, M.2    Wolfson, H.J.3    Nussinov, R.4
  • 13
    • 0033621104 scopus 로고    scopus 로고
    • Folding and binding cascades: Shifts in energy landscapes
    • Tsai CJ, Ma B, Nussinov R (1999) Folding and binding cascades: Shifts in energy landscapes. Proc Natl Acad Sci USA 96:9970-9972.
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 9970-9972
    • Tsai, C.J.1    Ma, B.2    Nussinov, R.3
  • 14
    • 0030810528 scopus 로고    scopus 로고
    • A monoclonal antibody induces opening of a coiled coil. Global protection of amide protons from H/D exchange decreases by up to 1000-fold in antibody-bound triple-stranded coiled coil
    • Durr E, Bosshard HR (1997) A monoclonal antibody induces opening of a coiled coil. Global protection of amide protons from H/D exchange decreases by up to 1000-fold in antibody-bound triple-stranded coiled coil. Eur J Biochem 249:325-329.
    • (1997) Eur J Biochem , vol.249 , pp. 325-329
    • Durr, E.1    Bosshard, H.R.2
  • 15
    • 78651189765 scopus 로고
    • On the nature of allosteric transitions: A plausible model
    • Monod J, Wyman J, Changeux JP (1965) On the nature of allosteric transitions: A plausible model. J Mol Biol 12:88-118.
    • (1965) J Mol Biol , vol.12 , pp. 88-118
    • Monod, J.1    Wyman, J.2    Changeux, J.P.3
  • 16
    • 21244440196 scopus 로고    scopus 로고
    • Conservation of μs-ms enzyme motions in the apo- and substrate-mimicked state
    • Beach H, Cole R, Gill ML, Loria JP (2005) Conservation of μs-ms enzyme motions in the apo- and substrate-mimicked state. J Am Chem Soc 127:9167-9176.
    • (2005) J Am Chem Soc , vol.127 , pp. 9167-9176
    • Beach, H.1    Cole, R.2    Gill, M.L.3    Loria, J.P.4
  • 17
    • 33644556820 scopus 로고    scopus 로고
    • Enzyme dynamics along the reaction coordinate: Critical role of a conserved residue
    • Kovrigin EL, Loria JP (2006) Enzyme dynamics along the reaction coordinate: Critical role of a conserved residue. Biochemistry 45:2636-2647.
    • (2006) Biochemistry , vol.45 , pp. 2636-2647
    • Kovrigin, E.L.1    Loria, J.P.2
  • 18
    • 27744499156 scopus 로고    scopus 로고
    • Intrinsic dynamics of an enzyme underlies catalysis
    • Eisenmesser EZ, et al. (2005) Intrinsic dynamics of an enzyme underlies catalysis. Nature 438:117-121.
    • (2005) Nature , vol.438 , pp. 117-121
    • Eisenmesser, E.Z.1
  • 19
    • 0035928796 scopus 로고    scopus 로고
    • Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism
    • Osborne MJ, Schnell J, Benkovic SJ, Dyson HJ, Wright PE (2001) Backbone dynamics in dihydrofolate reductase complexes: Role of loop flexibility in the catalytic mechanism. Biochemistry 40:9846-9859.
    • (2001) Biochemistry , vol.40 , pp. 9846-9859
    • Osborne, M.J.1    Schnell, J.2    Benkovic, S.J.3    Dyson, H.J.4    Wright, P.E.5
  • 20
    • 0019889093 scopus 로고
    • On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase
    • Alber T, et al. (1981) On the three-dimensional structure and catalytic mechanism of triose phosphate isomerase. Philos Trans R Soc Lond B Biol Sci 293:159-171.
    • (1981) Philos Trans R Soc Lond B Biol Sci , vol.293 , pp. 159-171
    • Alber, T.1
  • 21
    • 0016810498 scopus 로고
    • Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data
    • Banner DW, et al. (1975) Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data. Nature 255:609-614.
    • (1975) Nature , vol.255 , pp. 609-614
    • Banner, D.W.1
  • 22
    • 0023868490 scopus 로고
    • Reconstruction by site-directed mutagenesis of the transition state for the activation of tyrosine by the tyrosyl-tRNA synthetase: Amobile loop envelopes the transition state in an induced-fit mechanism
    • Fersht AR, Knill-Jones JW, Bedouelle H, Winter G (1988) Reconstruction by site-directed mutagenesis of the transition state for the activation of tyrosine by the tyrosyl-tRNA synthetase: Amobile loop envelopes the transition state in an induced-fit mechanism. Biochemistry 27:1581-1587.
    • (1988) Biochemistry , vol.27 , pp. 1581-1587
    • Fersht, A.R.1    Knill-Jones, J.W.2    Bedouelle, H.3    Winter, G.4
  • 23
    • 0025331920 scopus 로고
    • Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: Implications for catalysis
    • Lolis E, Petsko GA (1990) Crystallographic analysis of the complex between triosephosphate isomerase and 2-phosphoglycolate at 2.5-Å resolution: Implications for catalysis. Biochemistry 29:6619-6625.
    • (1990) Biochemistry , vol.29 , pp. 6619-6625
    • Lolis, E.1    Petsko, G.A.2
  • 24
    • 0037422593 scopus 로고    scopus 로고
    • Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2-Å resolution
    • Jogl G, Rozovsky S, McDermott AE, Tong L (2003) Optimal alignment for enzymatic proton transfer: Structure of the Michaelis complex of triosephosphate isomerase at 1.2-Å resolution. Proc Natl Acad Sci USA 100:50-55.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 50-55
    • Jogl, G.1    Rozovsky, S.2    McDermott, A.E.3    Tong, L.4
  • 25
    • 0025276041 scopus 로고
    • Stabilization of a reaction intermediate as a catalytic device: Definition of the functional role of the flexible loop in triosephosphate isomerase
    • Pompliano DL, Peyman A, Knowles JR (1990) Stabilization of a reaction intermediate as a catalytic device: Definition of the functional role of the flexible loop in triosephosphate isomerase. Biochemistry 29:3186-3194.
    • (1990) Biochemistry , vol.29 , pp. 3186-3194
    • Pompliano, D.L.1    Peyman, A.2    Knowles, J.R.3
  • 26
    • 0026782489 scopus 로고
    • Segmental motion in catalysis: Investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase
    • Sampson NS, Knowles JR (1992) Segmental motion in catalysis: Investigation of a hydrogen bond critical for loop closure in the reaction of triosephosphate isomerase. Biochemistry 31:8488-8494.
    • (1992) Biochemistry , vol.31 , pp. 8488-8494
    • Sampson, N.S.1    Knowles, J.R.2
  • 27
    • 0025272834 scopus 로고
    • Mammalian and avian liver phosphoenolpyruvate carboxykinase - Alternate substrates and inhibition by analogs of oxaloacetate
    • Ash DE, Emig FA, Chowdhury SA, Satoh Y, Schramm VL (1990) Mammalian and avian liver phosphoenolpyruvate carboxykinase - Alternate substrates and inhibition by analogs of oxaloacetate. J Biol Chem 265:7377-7384.
    • (1990) J Biol Chem , vol.265 , pp. 7377-7384
    • Ash, D.E.1    Emig, F.A.2    Chowdhury, S.A.3    Satoh, Y.4    Schramm, V.L.5
  • 28
    • 39649124209 scopus 로고    scopus 로고
    • Differential inhibition of cytosolic PEPCK by substrate analogues. Kinetic and structural characterization of inhibitor recognition
    • Stiffin R, M, Sullivan SM, Carlson GM, Holyoak T (2008) Differential inhibition of cytosolic PEPCK by substrate analogues. Kinetic and structural characterization of inhibitor recognition. Biochemistry 47:2099-2109.
    • (2008) Biochemistry , vol.47 , pp. 2099-2109
    • Stiffin, R.M.1    Sullivan, S.M.2    Carlson, G.M.3    Holyoak, T.4
  • 29
    • 33745814413 scopus 로고    scopus 로고
    • Structural insights into the mechanism of PEPCK catalysis
    • Holyoak T, Sullivan SM, Nowak T (2006) Structural insights into the mechanism of PEPCK catalysis. Biochemistry 45:8254-8263.
    • (2006) Biochemistry , vol.45 , pp. 8254-8263
    • Holyoak, T.1    Sullivan, S.M.2    Nowak, T.3
  • 30
    • 0023055771 scopus 로고
    • Stereochemical course of thiophosphoryl transfer catalyzed by cytosolic phosphoenolpyruvate carboxykinase
    • Konopka JM, Lardy HA, Frey PA (1986) Stereochemical course of thiophosphoryl transfer catalyzed by cytosolic phosphoenolpyruvate carboxykinase. Biochemistry 25:5571-5575.
    • (1986) Biochemistry , vol.25 , pp. 5571-5575
    • Konopka, J.M.1    Lardy, H.A.2    Frey, P.A.3
  • 31
    • 0021759420 scopus 로고
    • Stereochemical course of thiophosphoryl group transfer catalyzed by mitochondrial phosphoenolpyruvate carboxykinase
    • Sheu KF, et al. (1984) Stereochemical course of thiophosphoryl group transfer catalyzed by mitochondrial phosphoenolpyruvate carboxykinase. Biochemistry 23:1779-1783.
    • (1984) Biochemistry , vol.23 , pp. 1779-1783
    • Sheu, K.F.1
  • 32
    • 34548509216 scopus 로고    scopus 로고
    • Structures of rat cytosolic PEPCK: Insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid
    • Sullivan SM, Holyoak T (2007) Structures of rat cytosolic PEPCK: Insight into the mechanism of phosphorylation and decarboxylation of oxaloacetic acid. Biochemistry 46:10078-10088.
    • (2007) Biochemistry , vol.46 , pp. 10078-10088
    • Sullivan, S.M.1    Holyoak, T.2
  • 33
    • 0027751260 scopus 로고
    • Mutational and kinetic analysis of a mobile loop in tyrosyl-tRNA synthetase
    • First EA, Fersht AR (1993) Mutational and kinetic analysis of a mobile loop in tyrosyl-tRNA synthetase. Biochemistry 32:13658-13663.
    • (1993) Biochemistry , vol.32 , pp. 13658-13663
    • First, E.A.1    Fersht, A.R.2
  • 34
    • 0025015392 scopus 로고
    • Anatomy of a conformational change: Hinged "lid" motion of the triosephosphate isomerase loop
    • Joseph D, Petsko GA, Karplus M (1990) Anatomy of a conformational change: Hinged "lid" motion of the triosephosphate isomerase loop. Science 249:1425-1428.
    • (1990) Science , vol.249 , pp. 1425-1428
    • Joseph, D.1    Petsko, G.A.2    Karplus, M.3
  • 35
    • 18444386228 scopus 로고    scopus 로고
    • Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site
    • Dunten P, et al. (2002) Crystal structure of human cytosolic phosphoenolpyruvate carboxykinase reveals a new GTP-binding site. J Mol Biol 316:257-264.
    • (2002) J Mol Biol , vol.316 , pp. 257-264
    • Dunten, P.1
  • 36
    • 21844443838 scopus 로고    scopus 로고
    • Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop
    • Cotelesage JJH, Prasad L, Zeikus JG, Laivenieks M, Delbaere LTJ (2005) Crystal structure of Anaerobiospirillum succiniciproducens PEP carboxykinase reveals an important active site loop. Int J Biochem Cell Biol 37:1829.
    • (2005) Int J Biochem Cell Biol , vol.37 , pp. 1829
    • Cotelesage, J.J.H.1    Prasad, L.2    Zeikus, J.G.3    Laivenieks, M.4    Delbaere, L.T.J.5
  • 37
    • 0016255660 scopus 로고
    • Kinetic and magnetic resonance studies of the interaction of oxalate with pyruvate kinase
    • Reed GH, Morgan SD (1974) Kinetic and magnetic resonance studies of the interaction of oxalate with pyruvate kinase. Biochemistry 13:3537-3541.
    • (1974) Biochemistry , vol.13 , pp. 3537-3541
    • Reed, G.H.1    Morgan, S.D.2
  • 38
    • 0016232066 scopus 로고
    • Catalysis, binding and enzyme-substrate complementarity
    • Fersht AR (1974) Catalysis, binding and enzyme-substrate complementarity. Proc R Soc Lond B Biol Sci 187:397-407.
    • (1974) Proc R Soc Lond B Biol Sci , vol.187 , pp. 397-407
    • Fersht, A.R.1
  • 39
    • 0345894320 scopus 로고    scopus 로고
    • Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation
    • Desamero R, Rozovsky S, Zhadin N, McDermott A, Callender R (2003) Active site loop motion in triosephosphate isomerase: T-jump relaxation spectroscopy of thermal activation. Biochemistry 42:2941-2951.
    • (2003) Biochemistry , vol.42 , pp. 2941-2951
    • Desamero, R.1    Rozovsky, S.2    Zhadin, N.3    McDermott, A.4    Callender, R.5
  • 40
    • 0028049327 scopus 로고
    • Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis
    • Falzone CJ, Wright PE, Benkovic SJ (1994) Dynamics of a flexible loop in dihydrofolate reductase from Escherichia coli and its implication for catalysis. Biochemistry 33:439-442.
    • (1994) Biochemistry , vol.33 , pp. 439-442
    • Falzone, C.J.1    Wright, P.E.2    Benkovic, S.J.3
  • 41
    • 0023187070 scopus 로고
    • The use of site-directed mutagenesis and time-resolved fluorescence spectroscopy to assign the fluorescence contributions of individual tryptophan residues in Bacillus stearothermophilus lactate dehydrogenase
    • Waldman AD, et al. (1987) The use of site-directed mutagenesis and time-resolved fluorescence spectroscopy to assign the fluorescence contributions of individual tryptophan residues in Bacillus stearothermophilus lactate dehydrogenase. Biochim Biophys Acta 913:66-71.
    • (1987) Biochim Biophys Acta , vol.913 , pp. 66-71
    • Waldman, A.D.1
  • 43
    • 0029000872 scopus 로고
    • Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand gated
    • Williams JC, McDermott AE (1995) Dynamics of the flexible loop of triosephosphate isomerase: The loop motion is not ligand gated. Biochemistry 34:8309-8319.
    • (1995) Biochemistry , vol.34 , pp. 8309-8319
    • Williams, J.C.1    McDermott, A.E.2
  • 44
    • 36749008588 scopus 로고    scopus 로고
    • Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism
    • Arora K, Brooks CL, III. (2007) Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism. Proc Natl Acad Sci USA 104:18496-18501.
    • (2007) Proc Natl Acad Sci USA , vol.104 , pp. 18496-18501
    • Arora, K.1    Brooks III, C.L.2
  • 45
    • 0023702575 scopus 로고
    • A unifying model of the thermodynamics of formation of dehydrogenase-ligand complexes
    • Fisher HF (1988) A unifying model of the thermodynamics of formation of dehydrogenase-ligand complexes. Adv Enzymol Relat Areas Mol Biol 61:1-46.
    • (1988) Adv Enzymol Relat Areas Mol Biol , vol.61 , pp. 1-46
    • Fisher, H.F.1
  • 46
    • 0016624901 scopus 로고
    • Binding energy, specificity, and enzymic catalysis: The circe effect
    • Jencks WP (1975) Binding energy, specificity, and enzymic catalysis: The circe effect. Adv Enzymol Relat Areas Mol Biol 43:219-410.
    • (1975) Adv Enzymol Relat Areas Mol Biol , vol.43 , pp. 219-410
    • Jencks, W.P.1
  • 48
    • 0031059866 scopus 로고    scopus 로고
    • Processing of X-ray diffraction data collected in oscillation mode
    • Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326.
    • (1997) Methods Enzymol , vol.276 , pp. 307-326
    • Otwinowski, Z.1    Minor, W.2
  • 49
    • 0000560808 scopus 로고    scopus 로고
    • MOLREP: An automated program for molecular replacement
    • Vagin A, Teplyakov A (1997) MOLREP: An automated program for molecular replacement. J Appl Crystallogr 30:1022-1025.
    • (1997) J Appl Crystallogr , vol.30 , pp. 1022-1025
    • Vagin, A.1    Teplyakov, A.2
  • 50
    • 0028103275 scopus 로고
    • The Ccp4 Suite: Programs for protein crystallography
    • Bailey S (1994) The Ccp4 Suite: Programs for protein crystallography. Acta Crystallogr D50:760-763.
    • (1994) Acta Crystallogr , vol.D50 , pp. 760-763
    • Bailey, S.1
  • 51
    • 13244281317 scopus 로고    scopus 로고
    • Coot: Model-building tools for molecular graphics
    • Emsley P, and Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D60: 2126-2132.
    • (2004) Acta Crystallogr , vol.D60 , pp. 2126-2132
    • Emsley, P.1    Cowtan, K.2
  • 52
    • 33646260450 scopus 로고    scopus 로고
    • Optimal description of a protein structure in terms of multiple groups undergoing TLS motion
    • Painter J, Merritt EA (2006) Optimal description of a protein structure in terms of multiple groups undergoing TLS motion. Acta Crystallogr D62:439-450.
    • (2006) Acta Crystallogr , vol.D62 , pp. 439-450
    • Painter, J.1    Merritt, E.A.2
  • 53
    • 33645158291 scopus 로고    scopus 로고
    • TLSMD web server for the generation of multi-group TLS models
    • Painter J, Merritt EA (2006) TLSMD web server for the generation of multi-group TLS models. J Appl Crystallogr 39:109-111.
    • (2006) J Appl Crystallogr , vol.39 , pp. 109-111
    • Painter, J.1    Merritt, E.A.2


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