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

DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3-OH and 5-PO₄ ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD to form a covalent ligase-(lysyl-N)–AMP intermediate and release pyrophosphate (PP_i) or nicotinamide mononucleotide. In step 2, AMP is transferred from ligase-adenylate to the 5-PO₄ 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 domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4 –1.8 Å resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to nonhomologous 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䡠ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PP_i leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg² that engages the ATP phosphate and a second metal that bridges the ATP and phosphates.