Active-Site Dynamics of SpvC Virulence Factor from Salmonella typhimurium and Density Functional Theory Study of Phosphothreonine Lyase Catalysis

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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 β-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 α-carbon by Lys136 and β-elimination of the phosphate leaving group. Key kinetic isotopic effects are predicted based on the truncated active-site model.
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