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AAT Bioquest

What is the mechanism of DNA ligase?

Posted March 26, 2024


Answer

DNA ligase is an enzyme that catalyzes the ligation reaction. The mechanism of DNA ligase involves three main steps or catalytic events: 

  1. Activation of DNA ligase - ATP (adenosine triphosphate) breaks down into AMP (adenosine monophosphate), releasing energy. The released AMP attaches to the amino group of the lysine residue present on the active site of the enzyme DNA ligase by phosphoramidite bond. This results in the formation of a ligase-AMP complex. This process is also known as adenylation of DNA ligase and is accompanied by the release of pyrophosphate. 
  2. Activation of 5’ phosphate in nicks - DNA ligase transfers the activated ligase-AMP complex to the 5’ phosphate end of the donor. The ligase enzyme is released when the AMP interacts with the phosphate group, activating the 5’ end of single-strand DNA. 
  3. DNA ligation - The 5’ phosphate group of the donor strand is linked to a 3’ hydroxyl group of the receptor strand, forming a phosphodiester bond. Free AMP and hydrogen ions are released and DNA and nicks are sealed. During the process 2 ATP molecules are consumed for the formation of a single phosphodiester bond. 
Additional resources

Kinetic Mechanism of Human DNA Ligase I Reveals Magnesium-dependent Changes in the Rate-limiting Step That Compromise Ligation Efficiency

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