Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates.
Publication Type:Journal Article
Source:J Biol Chem (2019)
<p>DNA ligases are the of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD to form a covalent ligase-(lysyl-Nζ)-AMP intermediate and release pyrophosphate (PP) or nicotinamide mononucleotide (NMN). In step 2, AMP is transferred from ligase-adenylate to the 5'-PO DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase (NTase) domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.6 Å resolution of LigD, an ATP-dependent DNA ligase dedicated to non-homologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 Å), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD•ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PP leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg that engages the ATP α phosphate and a second metal that bridges the ATP β and γ phosphates.</p>