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Publication Abstract from PubMed

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-Nzeta)-AMP intermediate and release pyrophosphate (PPi) or nicotinamide mononucleotide (NMN). 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 (NTase) domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.6 A resolution of Mycobacterium tuberculosis 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 A), 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 PPi leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg(2+) that engages the ATP alpha phosphate and a second metal that bridges the ATP beta and gamma phosphates.

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.,Unciuleac MC, Goldgur Y, Shuman S J Biol Chem. 2019 Feb 4. pii: RA119.007445. doi: 10.1074/jbc.RA119.007445. PMID:30718283^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.