메뉴 건너뛰기




Volumn 55, Issue 3, 2016, Pages 560-574

Dual Role of the Active Site Residues of Thermus thermophilus 3-Isopropylmalate Dehydrogenase: Chemical Catalysis and Domain Closure

Author keywords

[No Author keywords available]

Indexed keywords

ABSTRACTING; ACTIVATION ENERGY; CATALYSIS; CATALYST ACTIVITY; CRYSTAL STRUCTURE; ENZYMES; MOLECULAR DYNAMICS; MOLECULAR MODELING; QUANTUM THEORY; X RAY SCATTERING;

EID: 84956746406     PISSN: 00062960     EISSN: 15204995     Source Type: Journal    
DOI: 10.1021/acs.biochem.5b00839     Document Type: Article
Times cited : (2)

References (62)
  • 1
    • 65449134009 scopus 로고    scopus 로고
    • A lysine-tyrosine pair carries out acid-base chemistry in the metal ion-dependent pyridine dinucleotide-linked beta-hydroxyacid oxidative decarboxylases
    • Aktas, D. F. and Cook, P. F. (2009) A lysine-tyrosine pair carries out acid-base chemistry in the metal ion-dependent pyridine dinucleotide-linked beta-hydroxyacid oxidative decarboxylases Biochemistry 48, 3565-3577 10.1021/bi8022976
    • (2009) Biochemistry , vol.48 , pp. 3565-3577
    • Aktas, D.F.1    Cook, P.F.2
  • 2
    • 0042835774 scopus 로고    scopus 로고
    • Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism
    • Tao, X., Yang, Z., and Tong, L. (2003) Crystal structures of substrate complexes of malic enzyme and insights into the catalytic mechanism Structure 11, 1141-1150 10.1016/S0969-2126(03)00168-0
    • (2003) Structure , vol.11 , pp. 1141-1150
    • Tao, X.1    Yang, Z.2    Tong, L.3
  • 3
    • 77953147390 scopus 로고    scopus 로고
    • Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions
    • Malik, R. and Viola, R. E. (2010) Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions Acta Crystallogr., Sect. D: Biol. Crystallogr. 66, 673-684 10.1107/S0907444910008851
    • (2010) Acta Crystallogr., Sect. D: Biol. Crystallogr. , vol.66 , pp. 673-684
    • Malik, R.1    Viola, R.E.2
  • 4
    • 84866068233 scopus 로고    scopus 로고
    • Induced fit and the catalytic mechanism of isocitrate dehydrogenase
    • Goncalves, S., Miller, S. P., Carrondo, M. A., Dean, A. M., and Matias, P. M. (2012) Induced fit and the catalytic mechanism of isocitrate dehydrogenase Biochemistry 51, 7098-7115 10.1021/bi300483w
    • (2012) Biochemistry , vol.51 , pp. 7098-7115
    • Goncalves, S.1    Miller, S.P.2    Carrondo, M.A.3    Dean, A.M.4    Matias, P.M.5
  • 5
    • 0034053460 scopus 로고    scopus 로고
    • Evaluation by site-directed mutagenesis of aspartic acid residues in the metal site of pig heart NADP-dependent isocitrate dehydrogenase
    • Grodsky, N. B., Soundar, S., and Colman, R. F. (2000) Evaluation by site-directed mutagenesis of aspartic acid residues in the metal site of pig heart NADP-dependent isocitrate dehydrogenase Biochemistry 39, 2193-2200 10.1021/bi9919753
    • (2000) Biochemistry , vol.39 , pp. 2193-2200
    • Grodsky, N.B.1    Soundar, S.2    Colman, R.F.3
  • 6
    • 1542361158 scopus 로고    scopus 로고
    • Critical role of Lys212 and Tyr140 in porcine NADP-dependent isocitrate dehydrogenase
    • Kim, T.-K., Lee, P., and Colman, R. F. (2003) Critical role of Lys212 and Tyr140 in porcine NADP-dependent isocitrate dehydrogenase J. Biol. Chem. 278, 49323-49331 10.1074/jbc.M303781200
    • (2003) J. Biol. Chem. , vol.278 , pp. 49323-49331
    • Kim, T.-K.1    Lee, P.2    Colman, R.F.3
  • 7
    • 1542297722 scopus 로고    scopus 로고
    • Ligands of the Mn2+ bound to porcine mitochondrial NADP-dependent isocitrate dehydrogenase, as assessed by mutagenesis
    • Huang, Y. C., Grodsky, N. B., Kim, T. K., and Colman, R. F. (2004) Ligands of the Mn2+ bound to porcine mitochondrial NADP-dependent isocitrate dehydrogenase, as assessed by mutagenesis Biochemistry 43, 2821-2828 10.1021/bi030253f
    • (2004) Biochemistry , vol.43 , pp. 2821-2828
    • Huang, Y.C.1    Grodsky, N.B.2    Kim, T.K.3    Colman, R.F.4
  • 8
    • 14644404936 scopus 로고    scopus 로고
    • A catalytic triad is responsible for acid-base chemistry in the Ascaris suum NAD-malic enzyme
    • Karsten, W. E., Liu, D., Rao, G. S., Harris, B. G., and Cook, P. F. (2005) A catalytic triad is responsible for acid-base chemistry in the Ascaris suum NAD-malic enzyme Biochemistry 44, 3626-3635 10.1021/bi047826o
    • (2005) Biochemistry , vol.44 , pp. 3626-3635
    • Karsten, W.E.1    Liu, D.2    Rao, G.S.3    Harris, B.G.4    Cook, P.F.5
  • 9
    • 0028952279 scopus 로고
    • Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP+-dependent isocitrate dehydrogenase from Escherichia coli
    • Lee, M. E., Dyer, D. H., Klein, O. D., Bolduc, J. M., Stoddard, B. L., and Koshland, D. E., Jr. (1995) Mutational analysis of the catalytic residues lysine 230 and tyrosine 160 in the NADP+-dependent isocitrate dehydrogenase from Escherichia coli Biochemistry 34, 378-384 10.1021/bi00001a046
    • (1995) Biochemistry , vol.34 , pp. 378-384
    • Lee, M.E.1    Dyer, D.H.2    Klein, O.D.3    Bolduc, J.M.4    Stoddard, B.L.5    Koshland, D.E.6
  • 10
    • 0028803693 scopus 로고
    • The role of glutamate 87 in the kinetic mechanism of Thermus thermophilus isopropylmalate dehydrogenase
    • Dean, A. M. and Dvorak, L. (1995) The role of glutamate 87 in the kinetic mechanism of Thermus thermophilus isopropylmalate dehydrogenase Protein Sci. 4, 2156-2167 10.1002/pro.5560041022
    • (1995) Protein Sci. , vol.4 , pp. 2156-2167
    • Dean, A.M.1    Dvorak, L.2
  • 11
    • 0027504526 scopus 로고
    • Kinetic analysis on the substrate specificity of 3-isopropylmalate dehydrogenase
    • Miyazaki, K., Kakinuma, K., Terasawa, H., and Oshima, T. (1993) Kinetic analysis on the substrate specificity of 3-isopropylmalate dehydrogenase FEBS Lett. 332, 35-36 10.1016/0014-5793(93)80477-C
    • (1993) FEBS Lett. , vol.332 , pp. 35-36
    • Miyazaki, K.1    Kakinuma, K.2    Terasawa, H.3    Oshima, T.4
  • 12
    • 0034697068 scopus 로고    scopus 로고
    • Arg-94 is crucial to the catalysis of 3-isopropylmalate dehyrdogenase from Thermus thermophilus HB8
    • Fujita, M., Toyooka, Y., Tamegai, H., Eguchi, T., and Kakinuma, K. (2000) Arg-94 is crucial to the catalysis of 3-isopropylmalate dehyrdogenase from Thermus thermophilus HB8 J. Mol. Catal. B: Enzym. 9, 149-155 10.1016/S1381-1177(99)00091-0
    • (2000) J. Mol. Catal. B: Enzym. , vol.9 , pp. 149-155
    • Fujita, M.1    Toyooka, Y.2    Tamegai, H.3    Eguchi, T.4    Kakinuma, K.5
  • 13
    • 84910116408 scopus 로고    scopus 로고
    • Structural and Energetic Basis of Isopropylmalate Dehydrogenase Enzyme Catalysis
    • Palló, A., Oláh, J., Gráczer, E., Merli, A., Závodszky, P., Weiss, M. S., and Vas, M. (2014) Structural and Energetic Basis of Isopropylmalate Dehydrogenase Enzyme Catalysis FEBS J. 281, 5063-5076 10.1111/febs.13044
    • (2014) FEBS J. , vol.281 , pp. 5063-5076
    • Palló, A.1    Oláh, J.2    Gráczer, E.3    Merli, A.4    Závodszky, P.5    Weiss, M.S.6    Vas, M.7
  • 14
    • 79954549726 scopus 로고    scopus 로고
    • Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase
    • Gráczer, é., Merli, A., Singh, R. K., Karuppasamy, M., Závodszky, P., Weiss, M. S., and Vas, M. (2011) Atomic level description of the domain closure in a dimeric enzyme: Thermus thermophilus 3-isopropylmalate dehydrogenase Mol. BioSyst. 7, 1646-1659 10.1039/c0mb00346h
    • (2011) Mol. BioSyst. , vol.7 , pp. 1646-1659
    • Gráczer, É.1    Merli, A.2    Singh, R.K.3    Karuppasamy, M.4    Závodszky, P.5    Weiss, M.S.6    Vas, M.7
  • 15
    • 84907919370 scopus 로고    scopus 로고
    • Elements and modulation of functional dynamics
    • Gibbs, A. C. (2014) Elements and modulation of functional dynamics J. Med. Chem. 57, 7819-7837 10.1021/jm500325k
    • (2014) J. Med. Chem. , vol.57 , pp. 7819-7837
    • Gibbs, A.C.1
  • 16
    • 0035399478 scopus 로고    scopus 로고
    • Large scale domain movement in cytochrome bc(1): a new device for electron transfer in proteins
    • Darrouzet, E., Moser, C. C., Dutton, P. L., and Daldal, F. (2001) Large scale domain movement in cytochrome bc(1): a new device for electron transfer in proteins Trends Biochem. Sci. 26, 445-451 10.1016/S0968-0004(01)01897-7
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 445-451
    • Darrouzet, E.1    Moser, C.C.2    Dutton, P.L.3    Daldal, F.4
  • 17
    • 79951987469 scopus 로고    scopus 로고
    • Time-dependent FRET with single enzymes: domain motions and catalysis in H(+)-ATP synthases
    • Bienert, R., Zimmermann, B., Rombach-Riegraf, V., and Graber, P. (2011) Time-dependent FRET with single enzymes: domain motions and catalysis in H(+)-ATP synthases ChemPhysChem 12, 510-517 10.1002/cphc.201000921
    • (2011) ChemPhysChem , vol.12 , pp. 510-517
    • Bienert, R.1    Zimmermann, B.2    Rombach-Riegraf, V.3    Graber, P.4
  • 18
    • 77952906090 scopus 로고    scopus 로고
    • Lessons learned from UvrD helicase: mechanism for directional movement
    • Yang, W. (2010) Lessons learned from UvrD helicase: mechanism for directional movement Annu. Rev. Biophys. 39, 367-385 10.1146/annurev.biophys.093008.131415
    • (2010) Annu. Rev. Biophys. , vol.39 , pp. 367-385
    • Yang, W.1
  • 19
    • 0036283942 scopus 로고    scopus 로고
    • Molecular dynamics of acetylcholinesterase
    • Shen, T., Tai, K., Henchman, R. H., and McCammon, J. A. (2002) Molecular dynamics of acetylcholinesterase Acc. Chem. Res. 35, 332-340 10.1021/ar010025i
    • (2002) Acc. Chem. Res. , vol.35 , pp. 332-340
    • Shen, T.1    Tai, K.2    Henchman, R.H.3    McCammon, J.A.4
  • 21
    • 38149070214 scopus 로고    scopus 로고
    • Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases
    • Kannan, N., Neuwald, A. F., and Taylor, S. S. (2008) Analogous regulatory sites within the alphaC-beta4 loop regions of ZAP-70 tyrosine kinase and AGC kinases Biochim. Biophys. Acta, Proteins Proteomics 1784, 27-32 10.1016/j.bbapap.2007.09.007
    • (2008) Biochim. Biophys. Acta, Proteins Proteomics , vol.1784 , pp. 27-32
    • Kannan, N.1    Neuwald, A.F.2    Taylor, S.S.3
  • 23
    • 77950170511 scopus 로고    scopus 로고
    • Insight into the mechanism of domain movements and their role in enzyme function: example of 3-phosphoglycerate kinase
    • Vas, M., Varga, A., and Gráczer, é. (2010) Insight into the mechanism of domain movements and their role in enzyme function: example of 3-phosphoglycerate kinase Curr. Protein Pept. Sci. 11, 118-147 10.2174/138920310790848403
    • (2010) Curr. Protein Pept. Sci. , vol.11 , pp. 118-147
    • Vas, M.1    Varga, A.2    Gráczer, É.3
  • 24
    • 84896727555 scopus 로고    scopus 로고
    • An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis
    • Palmai, Z., Seifert, C., Grater, F., and Balog, E. (2014) An allosteric signaling pathway of human 3-phosphoglycerate kinase from force distribution analysis PLoS Comput. Biol. 10, e1003444 10.1371/journal.pcbi.1003444
    • (2014) PLoS Comput. Biol. , vol.10
    • Palmai, Z.1    Seifert, C.2    Grater, F.3    Balog, E.4
  • 25
    • 84907855417 scopus 로고    scopus 로고
    • Phosphorylation- and nucleotide-binding-induced changes to the stability and hydrogen exchange patterns of JNK1beta1 provide insight into its mechanisms of activation
    • Owen, G. R., Stoychev, S., Achilonu, I., and Dirr, H. W. (2014) Phosphorylation- and nucleotide-binding-induced changes to the stability and hydrogen exchange patterns of JNK1beta1 provide insight into its mechanisms of activation J. Mol. Biol. 426, 3569-3589 10.1016/j.jmb.2014.08.019
    • (2014) J. Mol. Biol. , vol.426 , pp. 3569-3589
    • Owen, G.R.1    Stoychev, S.2    Achilonu, I.3    Dirr, H.W.4
  • 26
    • 0034049525 scopus 로고    scopus 로고
    • Structure of a closed form of human malic enzyme and implications for catalytic mechanism
    • Yang, Z., Floyd, D. L., Loeber, G., and Tong, L. (2000) Structure of a closed form of human malic enzyme and implications for catalytic mechanism Nat. Struct. Biol. 7, 251-257 10.1038/73378
    • (2000) Nat. Struct. Biol. , vol.7 , pp. 251-257
    • Yang, Z.1    Floyd, D.L.2    Loeber, G.3    Tong, L.4
  • 27
    • 1042275603 scopus 로고    scopus 로고
    • Exploring the range of protein flexibility, from a structural proteomics perspective
    • Gerstein, M. and Echols, N. (2004) Exploring the range of protein flexibility, from a structural proteomics perspective Curr. Opin. Chem. Biol. 8, 14-19 10.1016/j.cbpa.2003.12.006
    • (2004) Curr. Opin. Chem. Biol. , vol.8 , pp. 14-19
    • Gerstein, M.1    Echols, N.2
  • 28
    • 36549043024 scopus 로고    scopus 로고
    • Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation
    • Bahar, I., Chennubhotla, C., and Tobi, D. (2007) Intrinsic dynamics of enzymes in the unbound state and relation to allosteric regulation Curr. Opin. Struct. Biol. 17, 633-640 10.1016/j.sbi.2007.09.011
    • (2007) Curr. Opin. Struct. Biol. , vol.17 , pp. 633-640
    • Bahar, I.1    Chennubhotla, C.2    Tobi, D.3
  • 29
    • 36849039429 scopus 로고    scopus 로고
    • A hierarchy of timescales in protein dynamics is linked to enzyme catalysis
    • Henzler-Wildman, K. A., Lei, M., Thai, V., Kerns, S. J., Karplus, M., and Kern, D. (2007) A hierarchy of timescales in protein dynamics is linked to enzyme catalysis Nature 450, 913-916 10.1038/nature06407
    • (2007) Nature , vol.450 , pp. 913-916
    • Henzler-Wildman, K.A.1    Lei, M.2    Thai, V.3    Kerns, S.J.4    Karplus, M.5    Kern, D.6
  • 30
    • 61449109243 scopus 로고    scopus 로고
    • Symmetrical refolding of protein domains and subunits: example of the dimeric two-domain 3-isopropylmalate dehydrogenases
    • Gráczer, é., Varga, A., Melnik, B., Semisotnov, G., Závodszky, P., and Vas, M. (2009) Symmetrical refolding of protein domains and subunits: example of the dimeric two-domain 3-isopropylmalate dehydrogenases Biochemistry 48, 1123-1134 10.1021/bi801857t
    • (2009) Biochemistry , vol.48 , pp. 1123-1134
    • Gráczer, É.1    Varga, A.2    Melnik, B.3    Semisotnov, G.4    Závodszky, P.5    Vas, M.6
  • 31
    • 0014949207 scopus 로고
    • Cleavage of structural proteins during the assembly of the head of bacteriophage T4
    • Laemmli, U. K. (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4 Nature 227, 680-685 10.1038/227680a0
    • (1970) Nature , vol.227 , pp. 680-685
    • Laemmli, U.K.1
  • 32
    • 78651163419 scopus 로고
    • Disc Electrophoresis. I. Background and Theory
    • Ornstein, L. (1964) Disc Electrophoresis. I. Background and Theory Ann. N.Y. Acad. Sci. 121, 321-349
    • (1964) Ann. N.Y. Acad. Sci. , vol.121 , pp. 321-349
    • Ornstein, L.1
  • 33
    • 0141484613 scopus 로고    scopus 로고
    • PRIMUS: a Windows PC-based system for small-angle scattering data analysis
    • Konarev, P. V., Volkov, V. V., Sokolova, A. V., Koch, M. H. J., and Svergun, D. I. (2003) PRIMUS: a Windows PC-based system for small-angle scattering data analysis J. Appl. Crystallogr. 36, 1277-1282 10.1107/S0021889803012779
    • (2003) J. Appl. Crystallogr. , vol.36 , pp. 1277-1282
    • Konarev, P.V.1    Volkov, V.V.2    Sokolova, A.V.3    Koch, M.H.J.4    Svergun, D.I.5
  • 34
    • 0001498978 scopus 로고
    • La diffraction des rayons X aux trés petits angles; application á l'étude de phénoménes ultramicroscopiques
    • Guinier, A. (1939) La diffraction des rayons X aux trés petits angles; application á l'étude de phénoménes ultramicroscopiques Ann. Phys. 12, 166-237
    • (1939) Ann. Phys. , vol.12 , pp. 166-237
    • Guinier, A.1
  • 35
    • 0026910457 scopus 로고
    • Determination of the regularisation parameter in indirect-transform methods using perceptual criteria
    • Svergun, D. I. (1992) Determination of the regularisation parameter in indirect-transform methods using perceptual criteria J. Appl. Crystallogr. 25, 495-503 10.1107/S0021889892001663
    • (1992) J. Appl. Crystallogr. , vol.25 , pp. 495-503
    • Svergun, D.I.1
  • 36
    • 0029185933 scopus 로고
    • CRYSOL - a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates
    • Svergun, D. I., Barberato, C., and Koch, M. H. J. (1995) CRYSOL-a program to evaluate X-ray solution scattering of biological macromolecules from atomic coordinates J. Appl. Crystallogr. 28, 768-773 10.1107/S0021889895007047
    • (1995) J. Appl. Crystallogr. , vol.28 , pp. 768-773
    • Svergun, D.I.1    Barberato, C.2    Koch, M.H.J.3
  • 37
    • 80054088819 scopus 로고    scopus 로고
    • Essential role of the metal-ion in the IPM-assisted domain closure of 3-isopropylmalate dehydrogenase
    • Gráczer, é., Konarev, P. V., Szimler, T., Bacsó, A., Bodonyi, A., Svergun, D. I., Závodszky, P., and Vas, M. (2011) Essential role of the metal-ion in the IPM-assisted domain closure of 3-isopropylmalate dehydrogenase FEBS Lett. 585, 3297-3302 10.1016/j.febslet.2011.09.013
    • (2011) FEBS Lett. , vol.585 , pp. 3297-3302
    • Gráczer, É.1    Konarev, P.V.2    Szimler, T.3    Bacsó, A.4    Bodonyi, A.5    Svergun, D.I.6    Závodszky, P.7    Vas, M.8
  • 39
    • 0025743628 scopus 로고
    • Computer simulation and analysis of the reaction pathway of triosephosphate isomerase
    • Bash, P. A., Field, M. J., Davenport, R. C., Petsko, G. A., Ringe, D., and Karplus, M. (1991) Computer simulation and analysis of the reaction pathway of triosephosphate isomerase Biochemistry 30, 5826-5832 10.1021/bi00238a003
    • (1991) Biochemistry , vol.30 , pp. 5826-5832
    • Bash, P.A.1    Field, M.J.2    Davenport, R.C.3    Petsko, G.A.4    Ringe, D.5    Karplus, M.6
  • 40
    • 80455132317 scopus 로고    scopus 로고
    • Catalytic mechanism and roles of Arg197 and Thr183 in the Staphylococcus aureus sortase A enzyme
    • Tian, B. X. and Eriksson, L. A. (2011) Catalytic mechanism and roles of Arg197 and Thr183 in the Staphylococcus aureus sortase A enzyme J. Phys. Chem. B 115, 13003-13011 10.1021/jp2058113
    • (2011) J. Phys. Chem. B , vol.115 , pp. 13003-13011
    • Tian, B.X.1    Eriksson, L.A.2
  • 41
    • 84884907008 scopus 로고    scopus 로고
    • Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase
    • Liao, R. Z. and Thiel, W. (2013) Convergence in the QM-only and QM/MM modeling of enzymatic reactions: A case study for acetylene hydratase J. Comput. Chem. 34, 2389-2397 10.1002/jcc.23403
    • (2013) J. Comput. Chem. , vol.34 , pp. 2389-2397
    • Liao, R.Z.1    Thiel, W.2
  • 42
    • 84921626832 scopus 로고    scopus 로고
    • A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant
    • Perez-Gallegos, A., Garcia-Viloca, M., Gonzalez-Lafont, A., and Lluch, J. M. (2014) A QM/MM study of the associative mechanism for the phosphorylation reaction catalyzed by protein kinase A and its D166A mutant J. Comput.-Aided Mol. Des. 28, 1077-1091 10.1007/s10822-014-9786-3
    • (2014) J. Comput.-Aided Mol. Des. , vol.28 , pp. 1077-1091
    • Perez-Gallegos, A.1    Garcia-Viloca, M.2    Gonzalez-Lafont, A.3    Lluch, J.M.4
  • 43
    • 0344391945 scopus 로고    scopus 로고
    • Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase
    • Garcia-Viloca, M., Truhlar, D. G., and Gao, J. (2003) Reaction-path energetics and kinetics of the hydride transfer reaction catalyzed by dihydrofolate reductase Biochemistry 42, 13558-13575 10.1021/bi034824f
    • (2003) Biochemistry , vol.42 , pp. 13558-13575
    • Garcia-Viloca, M.1    Truhlar, D.G.2    Gao, J.3
  • 44
    • 53049102903 scopus 로고    scopus 로고
    • Physical nature of intermolecular interactions within cAMP-dependent protein kinase active site: differential transition state stabilization in phosphoryl transfer reaction
    • Szarek, P., Dyguda-Kazimierowicz, E., Tachibana, A., and Sokalski, W. A. (2008) Physical nature of intermolecular interactions within cAMP-dependent protein kinase active site: differential transition state stabilization in phosphoryl transfer reaction J. Phys. Chem. B 112, 11819-11826 10.1021/jp8040633
    • (2008) J. Phys. Chem. B , vol.112 , pp. 11819-11826
    • Szarek, P.1    Dyguda-Kazimierowicz, E.2    Tachibana, A.3    Sokalski, W.A.4
  • 45
    • 13444303958 scopus 로고    scopus 로고
    • How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study
    • Cheng, Y., Zhang, Y., and McCammon, J. A. (2005) How does the cAMP-dependent protein kinase catalyze the phosphorylation reaction: an ab initio QM/MM study J. Am. Chem. Soc. 127, 1553-1562 10.1021/ja0464084
    • (2005) J. Am. Chem. Soc. , vol.127 , pp. 1553-1562
    • Cheng, Y.1    Zhang, Y.2    McCammon, J.A.3
  • 47
    • 5644248354 scopus 로고    scopus 로고
    • Spin-forbidden CO ligand recombination in myoglobin
    • Harvey, J. N. (2004) Spin-forbidden CO ligand recombination in myoglobin Faraday Discuss. 127, 165-177 10.1039/b314768a
    • (2004) Faraday Discuss. , vol.127 , pp. 165-177
    • Harvey, J.N.1
  • 50
    • 79951476387 scopus 로고    scopus 로고
    • PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions
    • Olsson, M. H., Søndergaard, C. R., Rostkowski, M., and Jensen, J. H. (2011) PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa predictions J. Chem. Theory Comput. 7, 525-537 10.1021/ct100578z
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 525-537
    • Olsson, M.H.1    Søndergaard, C.R.2    Rostkowski, M.3    Jensen, J.H.4
  • 51
    • 79960258119 scopus 로고    scopus 로고
    • Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values
    • Søndergaard, C. R., Olsson, M. H., Rostkowski, M., and Jensen, J. H. (2011) Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values J. Chem. Theory Comput. 7, 2284-2295 10.1021/ct200133y
    • (2011) J. Chem. Theory Comput. , vol.7 , pp. 2284-2295
    • Søndergaard, C.R.1    Olsson, M.H.2    Rostkowski, M.3    Jensen, J.H.4
  • 52
    • 0027443645 scopus 로고
    • Tyr-139 in Thermus thermophilus 3-isopropylmalate dehydrogenase is involved in catalytic function
    • Miyazaki, K. and Oshima, T. (1993) Tyr-139 in Thermus thermophilus 3-isopropylmalate dehydrogenase is involved in catalytic function FEBS Lett. 332, 37-38 10.1016/0014-5793(93)80478-D
    • (1993) FEBS Lett. , vol.332 , pp. 37-38
    • Miyazaki, K.1    Oshima, T.2
  • 54
    • 0027534614 scopus 로고
    • Chemical mechanism of 6-phosphogluconate dehydrogenase from Candida utilis from pH studies
    • Berdis, A. J. and Cook, P. F. (1993) Chemical mechanism of 6-phosphogluconate dehydrogenase from Candida utilis from pH studies Biochemistry 32, 2041-2046 10.1021/bi00059a022
    • (1993) Biochemistry , vol.32 , pp. 2041-2046
    • Berdis, A.J.1    Cook, P.F.2
  • 55
    • 0030589731 scopus 로고    scopus 로고
    • Kinetic and chemical mechanisms of the sheep liver 6-phosphogluconate dehydrogenase
    • Price, N. E. and Cook, P. F. (1996) Kinetic and chemical mechanisms of the sheep liver 6-phosphogluconate dehydrogenase Arch. Biochem. Biophys. 336, 215-223 10.1006/abbi.1996.0551
    • (1996) Arch. Biochem. Biophys. , vol.336 , pp. 215-223
    • Price, N.E.1    Cook, P.F.2
  • 56
    • 84874984795 scopus 로고    scopus 로고
    • Structural, Kinetic and Chemical Mechanism of Isocitrate Dehydrogenase-1 from Mycobacterium tuberculosis
    • Quartararo, C. E., Hazra, S., Hadi, T., and Blanchard, J. S. (2013) Structural, Kinetic and Chemical Mechanism of Isocitrate Dehydrogenase-1 from Mycobacterium tuberculosis Biochemistry 52, 1765-1775 10.1021/bi400037w
    • (2013) Biochemistry , vol.52 , pp. 1765-1775
    • Quartararo, C.E.1    Hazra, S.2    Hadi, T.3    Blanchard, J.S.4
  • 57
    • 84920734436 scopus 로고    scopus 로고
    • Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase
    • Gráczer, é., Palló, A., Oláh, J., Szimler, T., Konarev, P. V., Svergun, D. I., Merli, A., Závodszky, P., Weiss, M. S., and Vas, M. (2015) Glutamate 270 plays an essential role in K(+)-activation and domain closure of Thermus thermophilus isopropylmalate dehydrogenase FEBS Lett. 589, 240-245 10.1016/j.febslet.2014.12.005
    • (2015) FEBS Lett. , vol.589 , pp. 240-245
    • Gráczer, É.1    Palló, A.2    Oláh, J.3    Szimler, T.4    Konarev, P.V.5    Svergun, D.I.6    Merli, A.7    Závodszky, P.8    Weiss, M.S.9    Vas, M.10
  • 58
    • 33748467645 scopus 로고    scopus 로고
    • Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase
    • Hayward, S. and Kitao, A. (2006) Molecular dynamics simulations of NAD+-induced domain closure in horse liver alcohol dehydrogenase Biophys. J. 91, 1823-1831 10.1529/biophysj.106.085910
    • (2006) Biophys. J. , vol.91 , pp. 1823-1831
    • Hayward, S.1    Kitao, A.2
  • 59
    • 34547103273 scopus 로고    scopus 로고
    • The effect of hinge mutations on effector binding and domain rotation in Escherichia coli D-3-phosphoglycerate dehydrogenase
    • Dey, S., Hu, Z., Xu, X. L., Sacchettini, J. C., and Grant, G. A. (2007) The effect of hinge mutations on effector binding and domain rotation in Escherichia coli D-3-phosphoglycerate dehydrogenase J. Biol. Chem. 282, 18418-18426 10.1074/jbc.M701174200
    • (2007) J. Biol. Chem. , vol.282 , pp. 18418-18426
    • Dey, S.1    Hu, Z.2    Xu, X.L.3    Sacchettini, J.C.4    Grant, G.A.5
  • 60
    • 51049093018 scopus 로고    scopus 로고
    • Intra- and intermonomer interactions are required to synergistically facilitate ATP hydrolysis in Hsp90
    • Cunningham, C. N., Krukenberg, K. A., and Agard, D. A. (2008) Intra- and intermonomer interactions are required to synergistically facilitate ATP hydrolysis in Hsp90 J. Biol. Chem. 283, 21170-21178 10.1074/jbc.M800046200
    • (2008) J. Biol. Chem. , vol.283 , pp. 21170-21178
    • Cunningham, C.N.1    Krukenberg, K.A.2    Agard, D.A.3
  • 61
    • 84896793115 scopus 로고    scopus 로고
    • Structural studies of yeast Delta(1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): active site flexibility and oligomeric state
    • Pemberton, T. A., Srivastava, D., Sanyal, N., Henzl, M. T., Becker, D. F., and Tanner, J. J. (2014) Structural studies of yeast Delta(1)-pyrroline-5-carboxylate dehydrogenase (ALDH4A1): active site flexibility and oligomeric state Biochemistry 53, 1350-1359 10.1021/bi500048b
    • (2014) Biochemistry , vol.53 , pp. 1350-1359
    • Pemberton, T.A.1    Srivastava, D.2    Sanyal, N.3    Henzl, M.T.4    Becker, D.F.5    Tanner, J.J.6
  • 62
    • 84876296940 scopus 로고    scopus 로고
    • Transient kinetic studies reveal isomerization steps along the kinetic pathway of Thermus thermophilus 3-isopropylmalate dehydrogenase
    • Gráczer, é., Lionne, C., Závodszky, P., Chaloin, L., and Vas, M. (2013) Transient kinetic studies reveal isomerization steps along the kinetic pathway of Thermus thermophilus 3-isopropylmalate dehydrogenase FEBS J. 280, 1764-1772 10.1111/febs.12191
    • (2013) FEBS J. , vol.280 , pp. 1764-1772
    • Gráczer, É.1    Lionne, C.2    Závodszky, P.3    Chaloin, L.4    Vas, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.