DNA Ligase

DNA ligase is an enzyme that catalyses the production of a phosphodiester bond between stands of DNA. For example it's the enzyme that closes the gaps between the Okazaki fragments on the lagging strand during DNA replication.

DNA Ligase I:  Connects Okazaki fragments of the lagging strand in DNA replication, and can also seal some repair and recombination fragments

DNA Ligase II: An alternatively spliced form of DNA ligase III that is only expressed in non-dividing cells.

DNA Ligase III: Works with protein XRCC1, which is a DNA repair protein. DNA ligase III is a primary agent in sealing base excision-repairs and recombination fragments.

DNA Ligase IV: Works with protein XRCC4, which is another DNA repair protein. DNA ligase IV is also crucial in sealing base excision-repairs and recombination fragments, especially during development. 

DNA Ligase Mechanism 

The mechanism of DNA ligase is to form two covalent phosphodiester bonds between 3' hydroxyl ends of one nucleotide with the 5' phosphate end of aonther. ATP is required for the for the ligase reaction, which proceeds in three steps:

1. Adenylation (addition of AMP): The side chain of lysine 34 in ligase forms a bond with ATP, where ATP gets rid of two phosphate groups to form an AMP-ligase complex.

2. Activation of 5’ phosphate: The monophosphate of the AMP-ligase complex forms a bond with the 5’ phosphate of the broken strand. This bonding activates the 5’ phosphate group for the next step.

3. Displacement of AMP connects the broken strand: The 5’ phosphate has been activated by the AMP-ligase complex, the 3’ hydroxyl group attacks the 5’ phosphate and forms a new bond, releasing the AMP. Ligase is crucial for holding the complex together in the necessary orientation. 

Breaking DNA

Environmental hazards can cause damage on DNA accidentally. For instance, Ionising radiation, such as gamma rays, attack the backbone of DNA and break the DNA. Human cells are also bathed with oxygen, a dangerous gas that forms reactive free radicals that attack DNA. Nonetheless, our cells also intentionally break our own DNA. During meiosis, the process where the genome is split into two halves for creation of egg or sperm cells, the DNA is often recombined. Portions of one DNA strand are cut out and traded with similar portions on a sister chromosome.

Repairing Broken DNA

DNA ligase reconnects DNA when they are broken. It uses a cofactor molecule for power and a special lysine amino acid to perform the reaction. DNA ligases from humans as well as from bacteriophage T7 use ATP as a cofactor. Many bacteria; however, use NAD in the reaction. In both cases, a lysine in the DNA ligase forms a bond to the phosphate in the cofactor, holding onto AMP portion and disgarding the rest. Later in the reaction, AMP is transferrrd to the broken DNA strand, and then is released when the strand is rejoned.