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 Journal Article
| Authors: | Unciuleac, M. C.; Goldgur, Y.; Shuman, S. |
| Article Title: | 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 |
| Abstract: | 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-PO 4 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-PO 4 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 Mg 2 that engages the ATP phosphate and a second metal that bridges the ATP and phosphates. © 2019 Unciuleac et al. Published under exclusive license by The American Society for Biochemistry and Molecular Biology, Inc. |
| Keywords: | mycobacterium tuberculosis; dna; dna replications; amino acids; phosphates; enzymes; transition state; leaving groups; nonhomologous end joining; complex networks; nicotinamide mononucleotide; open conformation; phosphodiester bonds |
| Journal Title: | Journal of Biological Chemistry |
| Volume: | 294 |
| Issue: | 13 |
| ISSN: | 0021-9258 |
| Publisher: | American Society for Biochemistry and Molecular Biology |
| Date Published: | 2019-03-29 |
| Start Page: | 5094 |
| End Page: | 5104 |
| Language: | English |
| DOI: | 10.1074/jbc.RA119.007445 |
| PUBMED: | 30718283 |
| PROVIDER: | scopus |
| PMCID: | PMC6442053 |
| DOI/URL: | |
| Notes: | Article -- Export Date: 1 May 2019 -- Source: Scopus |
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