Structure of the adenylation domain of an NAD(+)-dependent DNA ligase

Background: DNA ligases catalyse phosphodiester bond formation between adja cent bases in nicked DNA, thereby sealing the nick. A key step in the catal ytic mechanism is the formation of an adenylated DNA intermediate. The aden yl group is derived from either ATP (in eucaryotes and archaea) or NAD(+) ( in bacteria). This difference in cofactor specificity suggests that DNA lig ase may be a useful antibiotic target. Results: The crystal structure of the adenylation domain of the NAD(+)-depe ndent DNA ligase from Bacillus stearothermophilus has been determined at 2. 8 Angstrom resolution. Despite a complete lack of detectable sequence simil arity, the fold of the central core of this domain shares homology with the equivalent region of ATP-dependent DNA ligases, providing strong evidence for the location of the NAD(+)-binding site. Conclusions: Comparison of the structure of the NAD(+)-dependent DNA ligase with that of ATP-dependent ligases and mRNA-capping enzymes demonstrates t he manifold utilisation of a conserved nucleotidyltransferase domain within this family of enzymes. Whilst this conserved core domain retains a common mode of nucleotide binding and activation, it is the additional domains at the N terminus and/or the C terminus that provide the alternative specific ities and functionalities in the different members of this enzyme superfami ly.