Ligation reaction specificities of an NAD+-dependent DNA ligase from the hyperthermophile Aquifex aeolicus

An NAD(+)-dependent DNA ligase from the hyperthermophilic bacterium Aquifex aeolicus was cloned, expressed in Escherichia coli and purified to homogeneity, The enzyme is most active in slightly alkaline pH conditions with either Mg2+ or Mn2+ as the metal cofactor, Ca2+ and Ni2+ mainly support formation of DNA-adenylate intermediates. The catalytic cycle is characterized by a low k(cat) value of 2 min(-1) with concomitant accumulation of the DNA-adenylate intermediate when Mg2+ is used as the metal cofactor. The ligation rates of matched substrates vary by up to 4-fold, but exhibit a general trend of T/A less than or equal to G/C less than or equal to C/G less than or equal to A/T on both the 3'- and 5'-side of the nick. Consistent with previous studies on Thermus ligases, this Aquifex ligase exhibits greater discrimination against a mismatched base pair on the 3'-side of the nick junction. The requirement of 3' complementarity for a ligation reaction is reaffirmed by results from 1 nt insertions on either the 3'- or 5'-side of the nick, Furthermore, most of the unligatable 3' mismatched base pairs prohibit formation of the DNA-adenylate intermediate, indicating that the substrate adenylation step is also a control point for. ligation fidelity, Unlike previously studied ATP ligases, gapped substrates cannot be ligated and intermediate accumulation is minimal, suggesting that complete elimination of base pair complementarity on one side of the nick affects substrate adenylation on the 5'-side of the nick junction, Relationships among metal cofactors, ligation products and intermediate, and ligation fidelity ave discussed.