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Volumn 5, Issue SPEC ISS, 2004, Pages 141-153

The mechanism of phosphoryl transfer reaction and the role of active site residues on the basis of ribokinase-like kinases

Author keywords

Enzymatic catalysis; Phosphoryl transfer; Ribokinase like carbohydrate kinases; Static and dynamic catalytic fields

Indexed keywords

4 METHYL 5 BETA HYDROXYETHYLTHIAZOLE KINASE; PHOSPHOTRANSFERASE; RIBOKINASE; UNCLASSIFIED DRUG; ADENOSINE TRIPHOSPHATE; ARGININE; CARBOHYDRATE DERIVATIVE; CYSTEINE; MAGNESIUM ION; PHOSPHORUS DERIVATIVE; RIBOKINASE LIKE CARBOHYDRATE KINASE; THIAZOLE DERIVATIVE;

EID: 2942601110     PISSN: 14220067     EISSN: None     Source Type: Journal    
DOI: 10.3390/i5040141     Document Type: Conference Paper
Times cited : (13)

References (28)
  • 2
    • 0035078573 scopus 로고    scopus 로고
    • Structural basis for the ADP-specicity of a novel glucokinase from a hyperthermophilic archaeon
    • Ito, S.; Fushinobu, S.; Yoshioka, I.; Koga, S.; Matsuzawa, H.; Wakagi, T. Structural Basis for the ADP-Specicity of a Novel Glucokinase from a Hyperthermophilic Archaeon. Structure 2001, 9, 205-214.
    • (2001) Structure , vol.9 , pp. 205-214
    • Ito, S.1    Fushinobu, S.2    Yoshioka, I.3    Koga, S.4    Matsuzawa, H.5    Wakagi, T.6
  • 3
    • 0032506161 scopus 로고    scopus 로고
    • Structure of human adenosine kinase at 1.5Å resolution
    • Mathews, I. I.; Erion, M. D.; Ealick, S. E. Structure of Human Adenosine Kinase at 1.5Å Resolution. Biochemistry 1998, 37, 15607-15620.
    • (1998) Biochemistry , vol.37 , pp. 15607-15620
    • Mathews, I.I.1    Erion, M.D.2    Ealick, S.E.3
  • 4
    • 0034681294 scopus 로고    scopus 로고
    • Crystal structures of toxoplasma gondii adenosine kinase reveal a novel catalytic mechanism and prodrug binding
    • Schumacher, M. A.; Scott, D. M.; Mathews, I. I.; Ealick, S. E.; Roos, D. S.; Ullman, B.; Brennan R. G. Crystal Structures of Toxoplasma gondii Adenosine Kinase Reveal a Novel Catalytic Mechanism and Prodrug Binding. J. Mol. Biol. 2000, 296, 549-567.
    • (2000) J. Mol. Biol. , vol.296 , pp. 549-567
    • Schumacher, M.A.1    Scott, D.M.2    Mathews, I.I.3    Ealick, S.E.4    Roos, D.S.5    Ullman, B.6    Brennan, R.G.7
  • 5
    • 0032520213 scopus 로고    scopus 로고
    • Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8Å resolution: Insights into a new family of kinases tructures
    • Sigrell, J. A.; Cameron, A. D.; Jones, T. A.; Mowbray, S. L. Structure of Escherichia coli ribokinase in complex with ribose and dinucleotide determined to 1.8Å resolution: insights into a new family of kinases tructures. Structure 1998, 6, 183-193.
    • (1998) Structure , vol.6 , pp. 183-193
    • Sigrell, J.A.1    Cameron, A.D.2    Jones, T.A.3    Mowbray, S.L.4
  • 6
    • 2242483774 scopus 로고    scopus 로고
    • Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily
    • Li, M. H.; Kwok F.; Chang, W. R.; Lau, C. K.; Zhang, J. P.; Lo, S. C. L. ; Jiang, T.; Liang, D. C. Crystal structure of brain pyridoxal kinase, a novel member of the ribokinase superfamily. J. Biol. Chem. 2002, 277, 46385-46390.
    • (2002) J. Biol. Chem. , vol.277 , pp. 46385-46390
    • Li, M.H.1    Kwok, F.2    Chang, W.R.3    Lau, C.K.4    Zhang, J.P.5    Lo, S.C.L.6    Jiang, T.7    Liang, D.C.8
  • 7
    • 0034636799 scopus 로고    scopus 로고
    • Crystal structure of 4-methyl-5-β-hydroxyethylthiazole kinase from Bacillus subtilis at 1.5Å resolution
    • Campobasso, N.; Mathews I. I.; Begley, T. P.; Ealick, S. E. Crystal Structure of 4-Methyl-5-β-Hydroxyethylthiazole Kinase from Bacillus subtilis at 1.5Å Resolution. Biochemistry 2000, 39, 7868-7877.
    • (2000) Biochemistry , vol.39 , pp. 7868-7877
    • Campobasso, N.1    Mathews, I.I.2    Begley, T.P.3    Ealick, S.E.4
  • 8
    • 0036178687 scopus 로고    scopus 로고
    • Crystal structure of 4-amino-5-hydroxymethyl-2-methylpyrimidinephosphate kinase from Salmonella typhimurium at 2.3Å resolution
    • Cheng, G.; Bennett, E. M.; Begley, T. P.; Ealick, S. E. Crystal Structure of 4-Amino-5-Hydroxymethyl-2-Methylpyrimidinephosphate Kinase from Salmonella typhimurium at 2.3Å resolution. Structure 2002, 10, 225-235.
    • (2002) Structure , vol.10 , pp. 225-235
    • Cheng, G.1    Bennett, E.M.2    Begley, T.P.3    Ealick, S.E.4
  • 9
    • 0033545973 scopus 로고    scopus 로고
    • Dissection of the nucleotide and metal-phosphate binding sites in cAMP-dependent protein kinase
    • Herberg F. W.; Doyle M. L.; Cox S.; Taylor S. S. Dissection of the nucleotide and metal-phosphate binding sites in cAMP-dependent protein kinase. Biochemistry 1999, 38, 6352-6360.
    • (1999) Biochemistry , vol.38 , pp. 6352-6360
    • Herberg, F.W.1    Doyle, M.L.2    Cox, S.3    Taylor, S.S.4
  • 10
    • 0037454170 scopus 로고    scopus 로고
    • Mechanism of tyrosine phosphorylation catalyzed by the insulin receptor tyrosine kinase: A semiempirical PM3 study
    • Pichierri, F.; Matsuo, Y. Mechanism of tyrosine phosphorylation catalyzed by the insulin receptor tyrosine kinase: a semiempirical PM3 study. J. Mol. Struc.-Theochem 2003, 622, 257-267.
    • (2003) J. Mol. Struc.-Theochem. , vol.622 , pp. 257-267
    • Pichierri, F.1    Matsuo, Y.2
  • 12
    • 0242573649 scopus 로고    scopus 로고
    • ATP hydrolysis in water - A density functional study
    • Akola, J.; Jones, R. O. ATP Hydrolysis in Water - A Density Functional Study. J. Phys. Chem. B 2003, 107, 11774-11783.
    • (2003) J. Phys. Chem. B , vol.107 , pp. 11774-11783
    • Akola, J.1    Jones, R.O.2
  • 13
    • 0347899393 scopus 로고    scopus 로고
    • Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations
    • Diaz, N.; Field, M. J.; Insights into the phosphoryl-transfer mechanism of cAMP-dependent protein kinase from quantum chemical calculations and molecular dynamics simulations. J. Am. Chem. Soc. 2004, 126, 529-542.
    • (2004) J. Am. Chem. Soc. , vol.126 , pp. 529-542
    • Diaz, N.1    Field, M.J.2
  • 14
    • 0037030848 scopus 로고    scopus 로고
    • Quantum chemical study on the catalytic mechanism of the C-subunit of cAMP-dependent protein kinase
    • Hirano, Y.; Hata, M.; Hoshino, T.; Tsuda, M.; Quantum chemical study on the catalytic mechanism of the C-subunit of cAMP-dependent protein kinase. J. Phys. Chem. B 2002, 106, 5788-5792.
    • (2002) J. Phys. Chem. B , vol.106 , pp. 5788-5792
    • Hirano, Y.1    Hata, M.2    Hoshino, T.3    Tsuda, M.4
  • 15
    • 0000998079 scopus 로고
    • The effects of solvent on the conformation and the collective motions of protein - Normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum
    • Kitao, A.; Hirata, F.; Go, N.; The effects of solvent on the conformation and the collective motions of protein - normal mode analysis and molecular-dynamics simulations of melittin in water and in vacuum. Chem. Phys. 1991, 158, 447-472.
    • (1991) Chem. Phys. , vol.158 , pp. 447-472
    • Kitao, A.1    Hirata, F.2    Go, N.3
  • 16
    • 0141704162 scopus 로고    scopus 로고
    • Free energy landscape of protein folding in water: Explicit vs. implicit solvent
    • Zhou, RH.; Free energy landscape of protein folding in water: Explicit vs. implicit solvent Proteins 2003, 53, 148-161.
    • (2003) Proteins , vol.53 , pp. 148-161
    • Zhou, R.H.1
  • 17
    • 0141704726 scopus 로고    scopus 로고
    • Frisch, M. J.; et al. Gaussian, Inc., Pittsburgh PA
    • Gaussian 03, Revision B.04: Frisch, M. J.; et al. Gaussian, Inc., Pittsburgh PA, 2003.
    • (2003) Gaussian 03, Revision B.04
  • 18
    • 84988129057 scopus 로고
    • Optimization of parameters for semiempirical methods. 1. Method
    • Stewart, J. J. P. Optimization of parameters for semiempirical methods. 1. Method. J. Comput. Chem. 1989, 10, 209-220.
    • (1989) J. Comput. Chem. , vol.10 , pp. 209-220
    • Stewart, J.J.P.1
  • 19
    • 85005693478 scopus 로고
    • Combining synchronous transit and Quasi-Newton methods to find transition states
    • Peng, C. Y.; Schlegel H. B., Combining Synchronous Transit and Quasi-Newton Methods to Find Transition States. Israel J. Chem. 1993, 33, 449-454.
    • (1993) Israel J. Chem. , vol.33 , pp. 449-454
    • Peng, C.Y.1    Schlegel, H.B.2
  • 20
    • 2942617531 scopus 로고    scopus 로고
    • SCC DFT-TB energy calculations of the phosphoryl transfer reaction in the PKA active site
    • Rakowski F.; Grochowski P.; Lesyng B. SCC DFT-TB Energy calculations of the phosphoryl transfer reaction in the PKA active site. Cell. Mol. Biol. Lett. 2003, 8, 603-604.
    • (2003) Cell. Mol. Biol. Lett. , vol.8 , pp. 603-604
    • Rakowski, F.1    Grochowski, P.2    Lesyng, B.3
  • 21
    • 0022075532 scopus 로고
    • The physical nature of catalytic activity due to the molecular environment in terms of intermolecular interaction theory: Derivation of simplified models
    • Sokalski, W. A. The physical nature of catalytic activity due to the molecular environment in terms of intermolecular interaction theory: derivation of simplified models. J. Mol. Catalysis 1985, 30, 395-410.
    • (1985) J. Mol. Catalysis , vol.30 , pp. 395-410
    • Sokalski, W.A.1
  • 22
    • 77956691186 scopus 로고    scopus 로고
    • Leszczynski, J., Ed.; Elsevier Science; Chapter 10: Theoretical tools for analysis and modelling electrostatic effects in biomolecules
    • Sokalski, W. A.; Kedzierski, P.; Grembecka, J.; Dziekonski, P.; Strasburger K. In Computational Molecular Biology; Leszczynski, J., Ed.; Elsevier Science, 1999; Chapter 10: Theoretical tools for analysis and modelling electrostatic effects in biomolecules.; pp 369-391.
    • (1999) Computational Molecular Biology , pp. 369-391
    • Sokalski, W.A.1    Kedzierski, P.2    Grembecka, J.3    Dziekonski, P.4    Strasburger, K.5
  • 23
    • 0041457071 scopus 로고
    • Nonempirical modeling of the static and dynamic properties of the optimum environment for chemical reactions
    • Sokalski, W. A. Nonempirical modeling of the static and dynamic properties of the optimum environment for chemical reactions. J. Mol. Struct. 1986, 138, 77-87.
    • (1986) J. Mol. Struct. , vol.138 , pp. 77-87
    • Sokalski, W.A.1
  • 24
    • 0025390935 scopus 로고
    • Special issue - MOPAC - A semiempirical molecular-orbital program
    • Stewart, J. J. P. Special issue - MOPAC - a semiempirical molecular-orbital program. J. Comput. Aided Mol. Des. 1990, 4,1-45.
    • (1990) J. Comput. Aided Mol. Des. , vol.4 , pp. 1-45
    • Stewart, J.J.P.1
  • 25
    • 0030735466 scopus 로고    scopus 로고
    • A multidimensional driver for quantum chemistry program MOPAC
    • Cernohorsky, M.; Kuty, M.; Koca, J. A multidimensional driver for quantum chemistry program MOPAC. Comput. Chem. 1997, 21, 35-44.
    • (1997) Comput. Chem. , vol.21 , pp. 35-44
    • Cernohorsky, M.1    Kuty, M.2    Koca, J.3
  • 26
    • 0033671178 scopus 로고    scopus 로고
    • TRITON: In silico construction of protein mutants and prediction of their activities
    • Prokop, M.; Damborsky, J.; Koca, J. TRITON: in silico construction of protein mutants and prediction of their activities. Bioinformatics 2000, 16, 845-846.
    • (2000) Bioinformatics , vol.16 , pp. 845-846
    • Prokop, M.1    Damborsky, J.2    Koca, J.3
  • 27
    • 0035150226 scopus 로고    scopus 로고
    • TRITON: Graphic software for rational engineering of enzymes
    • Damborsky, J.; Prokop, M.; Koca, J. TRITON: graphic software for rational engineering of enzymes. Trends Biochem. Sci. 2001, 26, 71-73.
    • (2001) Trends Biochem. Sci. , vol.26 , pp. 71-73
    • Damborsky, J.1    Prokop, M.2    Koca, J.3
  • 28
    • 0031930594 scopus 로고    scopus 로고
    • Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A
    • Shaltiel, S.; Cox, S.; Taylor, S.S. Conserved water molecules contribute to the extensive network of interactions at the active site of protein kinase A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 484-491.
    • (1998) Proc. Natl. Acad. Sci. U.S.A. , vol.95 , pp. 484-491
    • Shaltiel, S.1    Cox, S.2    Taylor, S.S.3


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