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

Mihaela Carmen Unciuleac, Yehuda Goldgur, Stewart Shuman

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

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-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 (PPi) 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 PPi 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.

Original languageEnglish
Pages (from-to)5094-5104
Number of pages11
JournalJournal of Biological Chemistry
Volume294
Issue number13
DOIs
StatePublished - 29 Mar 2019
Externally publishedYes

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