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.