Analysis of an Anomalous Mutant of MutM DNA Glycosylase Leads to New Insights into the Catalytic Mechanism

Lesion-​specific DNA glycosylases play the key role in base-​excision DNA repair finding the damaged base and catalyzing its removal. Structural, computational, and exptl. studies have shown that MutM, a bacterial DNA glycosylase specific for 8-​oxoguanine (oxoG)​, encounters for oxoG lesion. The damaged nucleobase is extruded from the DNA and inserted into the enzyme active site, whereupon catalysis of glycosidic bond cleavage ensues. Here we show that the E3Q mutation provides substantial stabilization of oxoG in the active site of MutM. The simulations further show that oxoG is stabilized in the active site by protonation of the E3 carboxy group during the insertion process. It is also pointed out that the protonation could be significant for base-​excision catalysis. The results highlight the importance of accounting for the potential energetic and structural effects of mutations frequently introduced into enzymes to capture otherwise fleeting intermediates.