The catalytic mechanism of peptide deformylase enzymes containing zinc, iron, cobalt, and nickel dications was explored in the gas phase and in the protein environment. The study was performed at the density functional level using three model systems to simulate the active site. The work had the aim to evaluate the effect of metal substitution on the hydrolytic properties and the possible different performances of the various catalysts. Results indicated that all of the metallic forms are active to hydrolyze the formyl-peptide bond and that the reaction pathways do not show significant peculiarities on going from a particular metal ion to another. No significant modification of the reaction paths occurs in solvent.