6NHX

mycobacterial DNA ligase D complexed with ATP and MES

Summary for 6NHX

• Entry DOI: 10.2210/pdb6nhx/pdb
• Descriptor: ATP-dependent DNA ligase, ADENOSINE-5'-TRIPHOSPHATE, 2-(N-MORPHOLINO)-ETHANESULFONIC ACID, ... (4 entities in total)
• Functional Keywords: dna ligase, ligase
• Biological source: Mycobacterium tuberculosis
• Total number of polymer chains: 1
• Total formula weight: 34786.93

Authors

Shuman, S.,Unciuleac, M.,Goldgur, Y. (deposition date: 2018-12-24, release date: 2019-02-13, Last modification date: 2024-03-13)

Primary citation

Unciuleac, M.C.,Goldgur, Y.,Shuman, S.
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.
J. Biol. Chem., 294:5094-5104, 2019

PubMed Abstract: 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. 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 domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4-1.8 Å resolution of 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·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.

PubMed: 30718283
DOI: 10.1074/jbc.RA119.007445

Experimental method

X-RAY DIFFRACTION (1.4 Å)