title: Active-site dynamics of SpvC virulence factor from Salmonella typhimurium and density functional theory study of phosphothreonine lyase catalysis.
abstract: The newly discovered SpvC effector protein from Salmonella typhimurium interferes with the host immune response by dephosphorylating mitogen-activated protein kinases (MAPKs) with a beta-elimination mechanism. To understand this unique phosphothreonine lyase catalysis, the dynamics of the enzyme-substrate complex of the SpvC effector is investigated with a 3.2 ns molecular dynamics simulation, which reveals that the phosphorylated peptide substrate is tightly held in the active site by a hydrogen bond network and the lysine general base is positioned for the abstraction of the alpha hydrogen. The catalysis is further modeled with density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31+G(d,p) level of theory. The DFT calculations indicate the reaction proceeds via a single transition state, featuring a concerted proton abstraction from the alpha-carbon by Lys136 and beta-elimination of the phosphate leaving group. Key kinetic isotopic effects are predicted based on the truncated active-site model.
authors.affiliation: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131, USA.
authors.forename: Gregory K
authors.initials: GK
authors.lastname: Smith
authors.forename: Zhihong
authors.initials: Z
authors.lastname: Ke
authors.forename: Alvan C
authors.initials: AC
authors.lastname: Hengge
authors.forename: Dingguo
authors.initials: D
authors.lastname: Xu
authors.forename: Daiqian
authors.initials: D
authors.lastname: Xie
authors.forename: Hua
authors.initials: H
authors.lastname: Guo
mesh_terms: D019943:Amino Acid Substitution; D055162:Biocatalysis; D019757:Carbon-Oxygen Lyases / Q000737:chemistry* / Q000378:metabolism; D020134:Catalytic Domain; D006860:Hydrogen Bonding; D007700:Kinetics; D020928:Mitogen-Activated Protein Kinases / Q000378:metabolism; D056004:Molecular Dynamics Simulation; D016297:Mutagenesis, Site-Directed; D054730:Protein Interaction Domains and Motifs; D011994:Recombinant Proteins / Q000737:chemistry / Q000378:metabolism; D012486:Salmonella typhimurium / Q000201:enzymology*; D013816:Thermodynamics
chemical_list: D011994:Recombinant Proteins; D020928:Mitogen-Activated Protein Kinases; D019757:Carbon-Oxygen Lyases