3D Structure of DNA Ligase

CPK Color Scheme

Take a Tour of DNA Ligase!

These are the two distinct domains of DNA Ligase. The blue domain is the adenylation domain and contains the active site. The red domain is the OB fold domain, which enhances the adenylation activity of Domain 1. Click here. Notice the circular conformation of the enzyme to facilitate repair of nicked DNA.

DNA Ligase also has a Zinc finger, which is a common motif for DNA-binding proteins. Click here.

The Zinc finger consists of two beta sheets and an alpha helix. This area of the protein recognizes nicks in the DNA to facilitate ligase binding. Click here.

Now let's look at a molecule of DNA in the process of ligation. The gray molecule beside the DNA is AMP. Click here.

Zoom in on AMP. Click here.

Let's take a closer look at the nick in the DNA. Click here. AMP, in conjunction with ligase, is about to form a phosphodiester bond between the pink 3'-hydroxyl group to the blue 5'-phosphate group of the nicked DNA strand.

This is the active site of DNA Ligase. Amino acids are displayed as different colors. Click here.

Here we can see the critical amino acid in the active site, Lysine (blue), in its orientation to aid in repair of the nicked strand. The adenylation of lysine will cause the DNA-binding surface to rotate toward the active site. Click here.


Aidan, J., Suh, S. 2000. Structural and mechanistic conservation in DNA ligases. Nucleic Acids Research 28(21): 4051-58.

Tomkinson, A., Totty, N., Ginsburg, M., Lindahl, T. 1991. Location of the active sit for enzyme-adenylate formation in DNA ligases. Proc. Natl Acad. Sci. USA, 88: 400-404.