The crystal structure of the ATP-dependent DNA ligase from bacteriopha
ge T7 has been solved at 2.6 Angstrom resolution. The protein comprise
s two domains with a deep cleft running between them. The structure of
a complex with ATP reveals that the nucleotide binding pocket is situ
ated on the larger N-terminal domain, at the base of the cleft between
the two domains of the enzyme. Comparison of the overall domain struc
ture with that of DNA methyltransferases, coupled with other evidence,
suggests that DNA also binds in this cleft. Since this structure is t
he first of the nucleotidyl-transferase superfamily, which includes th
e eukaryotic mRNA capping enzymes, the relationship between the struct
ure of DNA ligase and that of other nucleotidyl-transferases is also d
iscussed.