Kinetics and thermodynamics of nick sealing by T4 DNA ligase

T4 DNA ligase is an Mg 2+ ‐dependent and ATP‐dependent enzyme that seals DNA nicks in three steps: it covalently binds AMP, transadenylates the nick phosphate, and catalyses formation of the phosphodiester bond releasing AMP. In this kinetic study, we further detail the reaction mechanism, showing that the overall ligation reaction is a superimposition of two parallel processes: a ‘processive’ ligation, in which the enzyme transadenylates and seals the nick without dissociating from dsDNA, and a ‘nonprocessive’ ligation, in which the enzyme takes part in the abortive adenylation cycle (covalent binding of AMP, transadenylation of the nick, and dissociation). At low concentrations of ATP (< 10 µ m ) and when the DNA nick is sealed with mismatching base pairs (e.g. five adjacent), this superimposition resolves into two kinetic phases, a burst ligation (≈ 0.2 min −1 ) and a subsequent slow ligation (≈ 2 × 10 −3 min −1 ). The relative rate and extent of each phase depend on the concentrations of ATP and Mg 2+ . The activation energies of self‐adenylation (16.2 kcal·mol −1 ), transadenylation of the nick (0.9 kcal·mol −1 ), and nick‐sealing (16.3–18.8 kcal·mol −1 ) were determined for several DNA substrates. The low activation energy of transadenylation implies that the transfer of AMP to the terminal DNA phosphate is a spontaneous reaction, and that the T4 DNA ligase–AMP complex is a high‐energy intermediate. To summarize current findings in the DNA ligation field, we delineate a kinetic mechanism of T4 DNA ligase catalysis.