Kinetic and thermodynamic analysis defines roles for two metal ions in DNA polymerase specificity and catalysis

Magnesium ions play a critical role in catalysis by many enzymes and contribute to the fidelity of DNA polymerases through a two-metal ion mechanism. However, specificity is a kinetic phenomenon and the roles of Mg²⁺ ions in each step in the catalysis have not been resolved. We first examined the roles of Mg²⁺ by kinetic analysis of single nucleotide incorporation catalyzed by HIV reverse transcriptase. We show that Mg.dNTP binding induces an enzyme conformational change at a rate that is independent of free Mg²⁺ concentration. Subsequently, the second Mg²⁺ binds to the closed state of the enzyme-DNA-Mg.dNTP complex (K_d = 3.7 mM) to facilitate catalysis. Weak binding of the catalytic Mg²⁺ contributes to fidelity by sampling the correctly aligned substrate without perturbing the equilibrium for nucleotide binding at physiological Mg²⁺ concentrations. An increase of the Mg²⁺ concentration from 0.25 to 10 mM increases nucleotide specificity (k_cat/K_m) 12-fold largely by increasing the rate of the chemistry relative to the rate of nucleotide release. Mg²⁺ binds very weakly (K_d ≤ 37 mM) to the open state of the enzyme. Analysis of published crystal structures showed that HIV reverse transcriptase binds only two metal ions prior to incorporation of a correct base pair. Molecular dynamics simulations support the two-metal ion mechanism and the kinetic data indicating weak binding of the catalytic Mg²⁺. Molecular dynamics simulations also revealed the importance of the divalent cation cloud surrounding exposed phosphates on the DNA. These results enlighten the roles of the two metal ions in the specificity of DNA polymerases.