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Literature summary for 3.5.1.88 extracted from

  • Xiao, C.; Zhang, Y.
    Catalytic mechanism and metal specificity of bacterial peptide deformylase: a density functional theory QM/MM study (2007), J. Phys. Chem. B, 111, 6229-6235.
    View publication on PubMed

Metals/Ions

Metals/Ions Comment Organism Structure
Fe2+ theoretically investigation of 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. 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 Escherichia coli
Zn2+ theoretically investigation of 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. 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 Escherichia coli

Organism

Organism UniProt Comment Textmining
Escherichia coli P0A6K3
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