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• W2098909980 startingPage "6229" @default.
• W2098909980 abstract "Bacterial peptide deformylase (PDF) represents a novel class of mononuclear iron peptidase, and has an intriguing metal preference different from most other metalloproteases. Using a hybrid density functional theory (B3LYP) QM/MM method, we have theoretically investigated its catalytic mechanism and metal specificity by studying both Fe2+-PDF and Zn2+-PDF. In both forms of PDF, the conserved Glu133 residue is protonated in the reactant complex, and acts as a general acid during the reaction. The initial reaction step is the nucleophilic attack of the metal-bound hydroxide on the carbonyl carbon of the substrate. Our calculations indicate that the metal ion in Fe2+-PDF is always pentacoordinated during the reaction process, while that in Zn2+-PDF is only tetrahedrally coordinated and not bound to the substrate in the reactant complex. This difference in their metal coordination is suggested to account for the lower activity of Zn2+-PDF in comparison with Fe2+-PDF." @default.
• W2098909980 created "2016-06-24" @default.
• W2098909980 creator A5040483619 @default.
• W2098909980 creator A5063629758 @default.
• W2098909980 date "2007-05-16" @default.
• W2098909980 modified "2023-10-16" @default.
• W2098909980 title "Catalytic Mechanism and Metal Specificity of Bacterial Peptide Deformylase: A Density Functional Theory QM/MM Study" @default.
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• W2098909980 doi "https://doi.org/10.1021/jp068657f" @default.
• W2098909980 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/17503802" @default.
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