메뉴 건너뛰기




Volumn 157, Issue 1-3, 2011, Pages 16-23

Computational investigation of the enzymatic mechanisms of phosphothreonine lyase

Author keywords

elimination; Michael addition; Phosphothreonine lyase; SpvC

Indexed keywords

BINDING PROTEIN; K136 PROTEIN; PHOSPHOTHREONINE; PHOSPHOTHREONINE LYASE; UNCLASSIFIED DRUG;

EID: 79957894774     PISSN: 03014622     EISSN: 18734200     Source Type: Journal    
DOI: 10.1016/j.bpc.2011.04.002     Document Type: Article
Times cited : (3)

References (44)
  • 1
    • 32944464648 scopus 로고    scopus 로고
    • Pathogen recognition and innate immunity
    • A. Shizuo, U. Satoshi, T. Osamu, Pathogen recognition and innate immunity, Cell 124 (2006) 783.
    • (2006) Cell , vol.124 , pp. 783
    • Shizuo, A.1    Satoshi, U.2    Osamu, T.3
  • 2
    • 33745530860 scopus 로고    scopus 로고
    • The many paths to p38 mitogen-activated protein kinase activation in the immune system
    • J.D. Ashwell, The many paths to p38 mitogen-activated protein kinase activation in the immune system, Nat. Rev. Immunol. 6 (2006) 532.
    • (2006) Nat. Rev. Immunol. , vol.6 , pp. 532
    • Ashwell, J.D.1
  • 3
    • 27144540463 scopus 로고    scopus 로고
    • Are innate immune signaling pathways in plants and animals conserved?
    • F.M. Ausubel, Are innate immune signaling pathways in plants and animals conserved? Nat. Immunol. 6 (2005) 973.
    • (2005) Nat. Immunol. , vol.6 , pp. 973
    • Ausubel, F.M.1
  • 6
    • 34248230244 scopus 로고    scopus 로고
    • Intercepting host MAPK signaling cascades by bacterial type III effectors
    • L. Shan, P. He, J. Sheen, Intercepting host MAPK signaling cascades by bacterial type III effectors, Cell Host Microbe 1 (2007) 167.
    • (2007) Cell Host Microbe , vol.1 , pp. 167
    • Shan, L.1    He, P.2    Sheen, J.3
  • 7
    • 33846958783 scopus 로고    scopus 로고
    • An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses
    • L. Arbibe, D.W. Kim, E. Batsche, T. Pedron, B. Mateescu, C. Muchardt, C. Parsot, P.J. Sansonetti, An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses, Nat. Immunol. 8 (2007) 47.
    • (2007) Nat. Immunol. , vol.8 , pp. 47
    • Arbibe, L.1    Kim, D.W.2    Batsche, E.3    Pedron, T.4    Mateescu, B.5    Muchardt, C.6    Parsot, C.7    Sansonetti, P.J.8
  • 9
    • 36749011295 scopus 로고    scopus 로고
    • Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase
    • Y. Zhu, H. Li, C. Long, L. Hu, H. Xu, L. Liu, S. Chen, D.-C. Wang, F. Shao, Structural insights into the enzymatic mechanism of the pathogenic MAPK phosphothreonine lyase, Mol. Cell 28 (2007) 899.
    • (2007) Mol. Cell , vol.28 , pp. 899
    • Zhu, Y.1    Li, H.2    Long, C.3    Hu, L.4    Xu, H.5    Liu, L.6    Chen, S.7    Wang, D.-C.8    Shao, F.9
  • 12
    • 33847154642 scopus 로고    scopus 로고
    • The phosphothreonine lyase activity of a bacterial type III effector family
    • H. Li, H. Xu, Y. Zhou, J. Zhang, C. Long, S. Li, S. Chen, J.-M. Zhou, F. Shao, The phosphothreonine lyase activity of a bacterial type III effector family, Science 315 (2007) 1000.
    • (2007) Science , vol.315 , pp. 1000
    • Li, H.1    Xu, H.2    Zhou, Y.3    Zhang, J.4    Long, C.5    Li, S.6    Chen, S.7    Zhou, J.-M.8    Shao, F.9
  • 13
    • 0033533601 scopus 로고    scopus 로고
    • Lysine-69 plays a key role in catalysis by ornithine decarboxylase through acceleration of the Schiff base formation, decarboxylation, and product release steps
    • A.L. Osterman, H.B. Brooks, L. Jackson, J.J. Abbott, M.A. Phillips, Lysine-69 plays a key role in catalysis by ornithine decarboxylase through acceleration of the Schiff base formation, decarboxylation, and product release steps, Biochemistry 38 (1999) 11814.
    • (1999) Biochemistry , vol.38 , pp. 11814
    • Osterman, A.L.1    Brooks, H.B.2    Jackson, L.3    Abbott, J.J.4    Phillips, M.A.5
  • 14
    • 33846644927 scopus 로고    scopus 로고
    • Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: Implications for an enzyme family
    • S. Kolappan, J. Zwahlen, R. Zhou, J.J. Truglio, P.J. Tonge, C. Kisker, Lysine 190 is the catalytic base in MenF, the menaquinone-specific isochorismate synthase from Escherichia coli: implications for an enzyme family, Biochemistry 46 (2007) 946.
    • (2007) Biochemistry , vol.46 , pp. 946
    • Kolappan, S.1    Zwahlen, J.2    Zhou, R.3    Truglio, J.J.4    Tonge, P.J.5    Kisker, C.6
  • 15
    • 0027291327 scopus 로고
    • Evidence that the catalytic activity of prokaryote leader peptidase depends upon the operation of a serine-lysine catalytic dyad
    • M.T. Black, Evidence that the catalytic activity of prokaryote leader peptidase depends upon the operation of a serine-lysine catalytic dyad, J. Bacteriol. 175 (1993) 4957.
    • (1993) J. Bacteriol. , vol.175 , pp. 4957
    • Black, M.T.1
  • 16
    • 33645306330 scopus 로고    scopus 로고
    • Suicide inhibition of alpha-oxamine synthases: Structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine
    • D. Alexeev, R. Baxter, D. Campopiano, O. Kerbarh, L. Sawyer, N. Tomczyk, R. Watt, S. Webster, Suicide inhibition of alpha-oxamine synthases: structures of the covalent adducts of 8-amino-7-oxononanoate synthase with trifluoroalanine, Org. Biomol. Chem. 4 (2006) 1209.
    • (2006) Org. Biomol. Chem. , vol.4 , pp. 1209
    • Alexeev, D.1    Baxter, R.2    Campopiano, D.3    Kerbarh, O.4    Sawyer, L.5    Tomczyk, N.6    Watt, R.7    Webster, S.8
  • 17
    • 69249158333 scopus 로고    scopus 로고
    • Radical triplets and suicide inhibition in reactions of 4-Thia-d- and 4-Thia-l-lysine with lysine 5,6-aminomutase
    • K.-H. Tang, S.O. Mansoorabadi, G.H. Reed, P.A. Frey, Radical triplets and suicide inhibition in reactions of 4-Thia-d- and 4-Thia-l-lysine with lysine 5,6-aminomutase, Biochemistry 48 (2009) 8151.
    • (2009) Biochemistry , vol.48 , pp. 8151
    • Tang, K.-H.1    Mansoorabadi, S.O.2    Reed, G.H.3    Frey, P.A.4
  • 19
    • 34848849542 scopus 로고    scopus 로고
    • 1. Antibiotic deactivation by a dizinc beta;-lactamase: Mechanistic insights from QM/MM and DFT studies
    • D. Xu, H. Guo, Q. Cui, 1. Antibiotic deactivation by a dizinc beta;-lactamase: mechanistic insights from QM/MM and DFT studies, J. Am. Chem. Soc. 129 (2007) 10814.
    • (2007) J. Am. Chem. Soc. , vol.129 , pp. 10814
    • Xu, D.1    Guo, H.2    Cui, Q.3
  • 20
    • 21244497608 scopus 로고    scopus 로고
    • Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis
    • R.A. Friesner, V. Guallar, Ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic catalysis, Annu. Rev. Phys. Chem. 56 (2005) 389.
    • (2005) Annu. Rev. Phys. Chem. , vol.56 , pp. 389
    • Friesner, R.A.1    Guallar, V.2
  • 22
    • 70449348216 scopus 로고    scopus 로고
    • The hydrolysis activity of adenosine triphosphate in myosin: A theoretical analysis of anomeric effects and the nature of the transition state
    • Y. Yang, Q. Cui, The hydrolysis activity of adenosine triphosphate in myosin: a theoretical analysis of anomeric effects and the nature of the transition state, J. Phys. Chem. A 113 (2009) 12439.
    • (2009) J. Phys. Chem. A , vol.113 , pp. 12439
    • Yang, Y.1    Cui, Q.2
  • 23
    • 75449116384 scopus 로고    scopus 로고
    • Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions
    • O. Acevedo, W.L. Jorgensen, Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions, Acc. Chem. Res. 43 (2010) 142.
    • (2010) Acc. Chem. Res. , vol.43 , pp. 142
    • Acevedo, O.1    Jorgensen, W.L.2
  • 24
    • 70349971100 scopus 로고    scopus 로고
    • Enzymatic catalysis: The emerging role of conceptual density functional theory
    • G. Roos, P. Geerlings, J. Messens, Enzymatic catalysis: the emerging role of conceptual density functional theory, J. Phys. Chem. B 113 (2009) 13465.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 13465
    • Roos, G.1    Geerlings, P.2    Messens, J.3
  • 28
    • 3142714765 scopus 로고    scopus 로고
    • Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations
    • A.D. MacKerell Jr., M. Feig, C.L. Brooks III, Extending the treatment of backbone energetics in protein force fields: Limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations, J. Comput. Chem. 25 (2004) 1400.
    • (2004) J. Comput. Chem. , vol.25 , pp. 1400
    • MacKerell Jr., A.D.1    Feig, M.2    Brooks III, C.L.3
  • 30
    • 0029860548 scopus 로고    scopus 로고
    • Structural characterization of the phosphotyrosine binding region of a high-affinity SH2 domain-phosphopeptide complex by molecular dynamics simulation and chemical shift calculations
    • M.-H. Feng, M. Philippopoulos, A.D. MacKerell, C. Lim, Structural characterization of the phosphotyrosine binding region of a high-affinity SH2 domain-phosphopeptide complex by molecular dynamics simulation and chemical shift calculations, J. Am. Chem. Soc. 118 (1996) 11265.
    • (1996) J. Am. Chem. Soc. , vol.118 , pp. 11265
    • Feng, M.-H.1    Philippopoulos, M.2    MacKerell, A.D.3    Lim, C.4
  • 31
    • 0031234042 scopus 로고    scopus 로고
    • An integral equation to describe the solvation of polar molecules in liquid water
    • D. Beglov, B. Roux, An integral equation to describe the solvation of polar molecules in liquid water, J. Phys. Chem. B 101 (1997) 7821.
    • (1997) J. Phys. Chem. B , vol.101 , pp. 7821
    • Beglov, D.1    Roux, B.2
  • 32
    • 33646940952 scopus 로고
    • Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of nalkanes
    • J.-P. Ryckaert, G. Ciccotti, H.J.C. Berendsen, Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of nalkanes, J. Comput. Phys. 23 (1977) 327.
    • (1977) J. Comput. Phys. , vol.23 , pp. 327
    • Ryckaert, J.-P.1    Ciccotti, G.2    Berendsen, H.J.C.3
  • 34
    • 53549117127 scopus 로고    scopus 로고
    • QM/QM studies for Michael reaction in corona virus main protease (3CLPro)
    • A.G. Taranto, P. Carvalho, M.A. Avery, QM/QM studies for Michael reaction in corona virus main protease (3CLPro), J. Mol. Graph. Mod. 27 (2008) 275.
    • (2008) J. Mol. Graph. Mod. , vol.27 , pp. 275
    • Taranto, A.G.1    Carvalho, P.2    Avery, M.A.3
  • 35
    • 34547456540 scopus 로고    scopus 로고
    • Antibiotic binding to dizinc β-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies
    • H. Guo, Q. Cui, Antibiotic binding to dizinc β-lactamase L1 from Stenotrophomonas maltophilia: SCC-DFTB/CHARMM and DFT studies, J. Phys. Chem. A 111 (2007) 5630.
    • (2007) J. Phys. Chem. A , vol.111 , pp. 5630
    • Guo, H.1    Cui, Q.2
  • 36
    • 4243553426 scopus 로고
    • Density-functional exchange-energy approximation with correct asymptotic behavior
    • A.D. Becke, Density-functional exchange-energy approximation with correct asymptotic behavior, Phys. Rev. A 38 (1988) 3098.
    • (1988) Phys. Rev. A , vol.38 , pp. 3098
    • Becke, A.D.1
  • 37
    • 0344718335 scopus 로고    scopus 로고
    • Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals
    • A.D. Becke, Density-functional thermochemistry. V. Systematic optimization of exchange-correlation functionals, J. Chem. Phys. 107 (1997) 8554.
    • (1997) J. Chem. Phys. , vol.107 , pp. 8554
    • Becke, A.D.1
  • 38
    • 0345491105 scopus 로고
    • Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density
    • C. Lee, W. Yang, R.G. Parr, Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density, Phys. Rev. B 37 (1988) 785.
    • (1988) Phys. Rev. B , vol.37 , pp. 785
    • Lee, C.1    Yang, W.2    Parr, R.G.3
  • 39
    • 6944251055 scopus 로고
    • Note on an approximation treatment for many-electron systems
    • C. Møller, M.S. Plesset, Note on an approximation treatment for many-electron systems, Phys. Rev. 46 (1934) 618.
    • (1934) Phys. Rev. , vol.46 , pp. 618
    • Møller, C.1    Plesset, M.S.2
  • 42
    • 66249136708 scopus 로고    scopus 로고
    • The origin of the electrostatic perturbation in acetoacetate decarboxylase
    • M.-C. Ho, J.-F. Menetret, H. Tsuruta, K.N. Allen, The origin of the electrostatic perturbation in acetoacetate decarboxylase, Nature 459 (2009) 393.
    • (2009) Nature , vol.459 , pp. 393
    • Ho, M.-C.1    Menetret, J.-F.2    Tsuruta, H.3    Allen, K.N.4
  • 43
    • 70449587040 scopus 로고    scopus 로고
    • Active-site dynamics of SpvC virulence factor from Salmonella typhimurium and density functional theory study of phosphothreonine lyase catalysis
    • G.K. Smith, Z. Ke, A.C. Hengge, D. Xu, D. Xie, H. Guo, Active-site dynamics of SpvC virulence factor from Salmonella typhimurium and density functional theory study of phosphothreonine lyase catalysis, J. Phys. Chem. B 113 (2009) 15327.
    • (2009) J. Phys. Chem. B , vol.113 , pp. 15327
    • Smith, G.K.1    Ke, Z.2    Hengge, A.C.3    Xu, D.4    Xie, D.5    Guo, H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.