Dynamic mechanism of nick recognition by DNA ligase
2002
DNA ligases are the enzymes responsible for the repair of singleâstranded and doubleâstranded nicks in dsDNA. DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNA has yet to be solved. DNA ligases share common structural elements with DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase–dsDNA interactions, we propose a mechanism for recognition of a singleâstranded nick by DNA ligase. According to this mechanism, ligase induces a BâtoâA DNA helix transition of the enzymeâbound dsDNA motif, which results in DNA contraction, bending and unwinding. For nonânicked dsDNA, this transition is reversible, leading to dissociation of the enzyme. For a nicked dsDNA substrate, the contraction of the enzymeâbound DNA motif (a) triggers an opened–closed conformational change of the enzyme, and (b) forces the motif to accommodate the strained A/Bâform hybrid conformation, in which the nicked strand tends to retain a Bâtype helix, while the nonânicked strand tends to form a shortened Aâtype helix. We propose that this conformation is the catalytically competent transition state, which leads to the formation of the DNA–AMP intermediate and to the subsequent sealing of the nick.
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