To determine the factors involved in the specific recognition function of a bacterial. 8-oxoguanine (oxoG) DNA glycosylase MutM, a series of potentials of mean force and thermodynamic integration simulations were performed with the wild type and a single-point E3Q mutant of MutM bound to oxoG and G-containing DNA, respectively. Interestingly, the mutation of the catalytically important Glu3 (E3) residue to Gin (Q) significantly changes the free-energy surface so that oxoG can bind stably in the active site of the enzyme, Free-energy simulations with the protonated and deprotonated E3 residue further showed that the protonation of the catalytically important E3 residue plays a key role in distinguishing oxoG versus G in the active site by lowering the free energy of oxoG preferentially in the active site. The results suggest that MutM utilizes the thermodynamic recognition mechanism for stable binding of the lesion base in the active site of the enzyme in addition to kinetic discrimination at the early stage of the base extrusion for facilitated extrusion of oxoG.