ArticleNucleic acids research2019
Structural intermediates of a DNA-ligase complex illuminate the role of the catalytic metal ion and mechanism of phosphodiester bond formation.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed, 23 citations in OpenAlex.
- Crystal structure of ATP-dependent DNA ligase from Rhizobium phage vB_RleM_P10VF.Acta crystallographica. Section F, Structural biology communications · 2025Article
- Four Parallel Pathways in T4 Ligase-Catalyzed Repair of Nicked DNA with Diverse Bending Angles.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- DNA repair enzymes of the Antarctic Dry Valley metagenome.Frontiers in microbiology · 2023Article
- Thermostable DNA ligases from hyperthermophiles in biotechnology.Frontiers in microbiology · 2023Review
- Kinetics and mechanism of formation of nickel(II)porphyrin and its interaction with DNA in aqueous medium.Journal of chemical sciences (Bangalore, India) · 2021Article
- Structural insight into DNA joining: from conserved mechanisms to diverse scaffolds.Nucleic acids research · 2020Review
- Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.Nucleic acids research · 2020Article
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Authors and funding
2 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
DNA ligases join adjacent 5' phosphate (5'P) and 3' hydroxyl (3'OH) termini of double-stranded DNA via a three-step mechanism requiring a nucleotide cofactor and divalent metal ion. Although considerable structural detail is available for the first two steps, less is known about step 3 where the DNA-backbone is joined or about the cation role at this step. We have captured high-resolution structures of an adenosine triphosphate (ATP)-dependent DNA ligase from Prochlorococcus marinus including a Mn-bound pre-ternary ligase-DNA complex poised for phosphodiester bond formation, and a post-ternary intermediate retaining product DNA and partially occupied AMP in the active site. The pre-ternary structure unambiguously identifies the binding site of the catalytic metal ion and confirms both its role in activating the 3'OH terminus for nucleophilic attack on the 5'P group and stabilizing the pentavalent transition state. The post-ternary structure indicates that DNA distortion and most enzyme-AMP contacts remain after phosphodiester bond formation, implying loss of covalent linkage to the DNA drives release of AMP, rather than active site rearrangement. Additionally, comparisons of this cyanobacterial DNA ligase with homologs from bacteria and bacteriophage pose interesting questions about the structural origin of double-strand break joining activity and the evolution of these ATP-dependent DNA ligase enzymes.
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