3D Structure of DNA Ligase

CPK Color Scheme

DNA Ligase is an essential enzyme within all cells that seals breaks in the phosphate-sugar backbone of DNA. DNA ligase accomplishs three main functions: joining Okazaki fragments, sealing repairs, and sealing recombination fragments (Purves et al., 2001).

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All eukaryotes and viruses have ligases that are ATP dependent, such as this one from the T7 bacteriophage. Let's take a look at ATP (click here) and its binding site in ligase. Click here. Ligase is colored blue and ATP is colored in the cpk color scheme illustrated above (Kogoy, 2003).

Let's take an even closer look at the ATP binding site. Click here. Notice how ATP is floating in the binding site of ligase directly next to lysine 34.

This spacial orientation is required before ATP and ligase can form a bond between the amino group of lysine 34's sidechain and the phosphate of AMP (loss of a diphosphate from ATP). Go to this webpage for more info on ligase's function and chemical mechanism: Molecular Tool: Ligation.

Once ATP binds to ligase, a diphosphate is released to allow AMP to bind to ligase (bond not shown). Click here.

This activated ligase transfers AMP (Click here) to a break in DNA, where it attaches AMP to the phosphate group. This activated phosphate group can now bind to its adjacent sugar to seal the break in the DNA backbone.





Kogoy, John. (2003). CPK Color Scheme. Permission to use granted.

Purves, W., Sadava, D., Orians, G., Heller, H. Life: The Science of Biology. Sinauer Associates, Inc., 2001.