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Following statements are being made about the mechanism of this reaction.
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Eduncle Best Answer
All DNA ligases catalyze the synthesis of phosphodiester bonds in a very similar manner, by esterification of a 5'-phosphoryl to a 3' hydroxyl group. The reaction mechanism can be split into three distinct catalytic events.
The first involves activation of the ligase through the formation of a covalent protein–AMP intermediate. The nucleotide has been shown to be linked to the enzyme through a phosphoramidate bond to the e amino group of a conserved active site lysine.
In the second step of the reaction, the AMP moiety is transferred from the ligase to the 5'-phosphate group at the single-strand break site.
Finally, DNA ligase catalyses the DNA ligation step with loss of free AMP.
In spite of these similarities between the two classes of enzymes, the manner by which the eubacterial and ‘eukaryotic’ proteins become activated is rather different.
For eukaryotic ligases, the enzyme–AMP complex is formed after reaction of the enzyme and ATP with the release of free pyrophosphate. The bacterial ligases become adenylated in an unusual reaction which involves cleavage of NAD+ and release of nicotinamide mononucleotide