27 by: Josie Cumming
Student – Josie Cumming
Enzyme – DNA Ligase
E.C. 6.5.1.1
DNA Ligase is an enzyme that is found in all organisms that contain DNA. It is found on the DNA strand, commonly during DNA replication, or on DNA sites that require repair.
DNA Ligase is responsible for sealing nicks in the DNA backbone by forming phosphodiester bonds within DNA’s phosphate-sugar backbone. Phosphodiester bonds are strong covalent bonds between the 3’-hydroxyl group of one sugar molecule in the backbone and the 5’-phosphate group of another sugar molecule. DNA Ligase catalyzes the creation of these phosphodiester bonds by first recognizing a nick in the backbone, or a broken phosphodiester bond. In eukaryotes, DNA Ligase utilizes an ATP molecule (NAD+ in Bacteria/Archaea) and forms a Ligase-AMP intermediate. This is accomplished by a Lysine 34A residue in DNA Ligase’s active site binding with the ATP to form a lysine-AMP intermediate. The AMP is then transferred through nucleophilic attack on the 5’-phosphate end of the DNA nick, which then causes the 3’-hydroxyl end to perform a nucleophilic attack on the 5’-phosphate DNA end. The AMP is discarded, and a phosphodiester bond remains. The nick is now sealed, and DNA Ligase continues down the DNA strand to fix any other nicks. Nicks are commonly found between Okazaki fragments on the lagging strand during DNA replication, as well as from physical handling during DNA recombination.
There are a few different types of DNA Ligases. The ATP-dependent DNA Ligases include Bacteriophage T4 DNA Ligase, and DNA Ligases I, III, and IV (all three found in mammals). The NAD+ dependent DNA Ligases are E.coli DNA Ligase and Taq DNA Ligase. While they all help to repair nicks in the backbone, they may have different methods to accomplish this. My video focuses mainly on DNA Ligase I.
References:
Addgene. 2022. Plasmids and recombinant DNA technology. Molecular biology reference. Addgene: Molecular Biology Reference
Britton S. 2024. Unraveling the process of DNA replication. Livius Prep. The DNA Replication Process Overview | Livius Prep
Elamparithi-Balu K., Gulkis M., Almohdar D., Caglayan M. 2024. Structures of LIG1 provide a mechanistic basis for understanding a lack of sugar discrimination against a ribonucleotide at the 3’-end of nick DNA. JBC Research Article. https://doi.org/10.1016/j.jbc.2024.107216.
Johnson, A., O’Donnell, M. 2005. DNA Ligase: getting a grip to seal the deal. Current Biology, 15(3), R90–R92. https://doi.org/10.1016/j.cub.2005.01.025.
National Human Genome Research Institute. Phosphate Backbone. Genome.gov; Phosphate Backbone (genome.gov)
Sallmyr A., Khattri-Bhandari S., Naila T., Tomkinson A.E. 2024. Mammalian DNA ligases; roles in maintaining genome integrity. University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine. https://doi.org/10.1016/j.jmb.2023.168276.
Taylor M.R., Conrad J.A., Wahl D., O’Brien P.J. 2011. Kinetic mechanisms of human DNA Ligase I reveals Magnesium-dependent changes in the rate-limiting step that compromise ligation efficiency. Journal of Biological Chemistry, Volume 286, Issue 26, 23054 – 23062. DOI 10.1074/jbc.M111.248831.
Winchester A.M. 2024. Encyclopedia Britannica, Genetics. Encyclopedia Britannica. DNA | Definition, Discovery, Function, Bases, Facts, & Structure | Britannica
