Comparison of Magnesium and Manganese Ions on the Structural and Catalytic Properties of Human DNA Polymerase Gamma

DNA polymerases are essential enzymes responsible for accurate genome replication and repair, with divalent metal cofactors playing a crucial role in their catalytic function. Polymerase γ (Pol γ) is the primary DNA polymerase in mitochondria, ensuring the faithful replication of mitochondrial DNA. The choice of metal cofactor, typically magnesium (Mg2+) or manganese (Mn2+), influences its structural stability, enzymatic activity, and fidelity. In this study, we employed molecular dynamics (MD) simulations and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations to investigate how Mg2+ and Mn2+ affect the flexibility, active site stabilization, and catalytic efficiency of Pol γ. Intermolecular interaction analysis of individual residues is consistent with experimental mutagenesis reports and highlights the importance of specific residues, many of which are evolutionarily conserved, and some are involved in pathogenic mutations. It is also observed that Mn2+ enhances catalytic efficiency, exhibiting higher exoergicity (−3.65 kcal mol–1 vs −1.61 kcal mol–1 for Mg2+) and a lower activation barrier. Intermolecular interaction analysis reveals that Mn2+ provides larger stabilization of the transition state and product complex, favoring reaction progression. Investigation of the effects of the electric field in the active site suggests that the O3′ atom on the DNA primer base experiences larger polarization in the system with Mn2+ ions when compared to Mg2+, with dipole directions consistent with the catalytic reaction progress. Our findings highlight a trade-off between structural stability and catalytic efficiency, providing insights into the role of metal ions in mitochondrial polymerase function and their implications for mutagenesis and mitochondrial disorders.