ArticleNucleic acids research2016
Kinetic mechanism and fidelity of nick sealing by Escherichia coli NAD+-dependent DNA ligase (LigA).
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 19 citations in OpenAlex.
- Codon usage bias analysis of the gene encoding NADArchives of microbiology · 2023Article
- Episomal and chromosomal DNA replication and recombination inFrontiers in molecular biosciences · 2023Review
- Alleviation of C⋅C Mismatches in DNA by theFrontiers in microbiology · 2021Article
- Cognate base-pair selectivity of hydrophobic unnatural bases in DNA ligation by T4 DNA ligase.Biopolymers · 2021Article
- Two-tiered enforcement of high-fidelity DNA ligation.Nature communications · 2019Article
- Single-molecule detection of deoxyribonucleoside triphosphates in microdroplets.Nucleic acids research · 2019Article
- A single-molecule sequencing assay for the comprehensive profiling of T4 DNA ligase fidelity and bias during DNA end-joining.Nucleic acids research · 2018Article
- Excision of the doubly methylated basePhilosophical transactions of the Royal Society of London. Series B, Biological sciences · 2018Article
- Crystal structure and mutational analysis of Mycobacterium smegmatis FenA highlight active site amino acids and three metal ions essential for flap endonuclease and 5' exonuclease activities.Nucleic acids research · 2018Article
- The Sole DNA Ligase inFrontiers in cellular and infection microbiology · 2018Article
- The DNA Repair Repertoire of Mycobacterium smegmatis FenA Includes the Incision of DNA 5' Flaps and the Removal of 5' Adenylylated Products of Aborted Nick Ligation.Journal of bacteriology · 2017Article
- Lethality of MalE-LacZ hybrid protein shares mechanistic attributes with oxidative component of antibiotic lethality.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Two-metal versus one-metal mechanisms of lysine adenylylation by ATP-dependent and NADProceedings of the National Academy of Sciences of the United States of America · 2017Article
- Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea.Bioscience reports · 2016Article
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Authors and funding
2 authors at 1 institution in 1 country.
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Abstract
Escherichia coli DNA ligase (EcoLigA) repairs 3'-OH/5'-PO4 nicks in duplex DNA via reaction of LigA with NAD(+) to form a covalent LigA-(lysyl-Nζ)-AMP intermediate (step 1); transfer of AMP to the nick 5'-PO4 to form an AppDNA intermediate (step 2); and attack of the nick 3'-OH on AppDNA to form a 3'-5' phosphodiester (step 3). A distinctive feature of EcoLigA is its stimulation by ammonium ion. Here we used rapid mix-quench methods to analyze the kinetic mechanism of single-turnover nick sealing by EcoLigA-AMP. For substrates with correctly base-paired 3'-OH/5'-PO4 nicks, kstep2 was fast (6.8-27 s(-1)) and similar to kstep3 (8.3-42 s(-1)). Absent ammonium, kstep2 and kstep3 were 48-fold and 16-fold slower, respectively. EcoLigA was exquisitely sensitive to 3'-OH base mispairs and 3' N:abasic lesions, which elicited 1000- to >20000-fold decrements in kstep2. The exception was the non-canonical 3' A:oxoG configuration, which EcoLigA accepted as correctly paired for rapid sealing. These results underscore: (i) how EcoLigA requires proper positioning of the nick 3' nucleoside for catalysis of 5' adenylylation; and (ii) EcoLigA's potential to embed mutations during the repair of oxidative damage. EcoLigA was relatively tolerant of 5'-phosphate base mispairs and 5' N:abasic lesions.
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