Tuesday, March 29, 2011

DNA Ligase: Literature Information

Original information for this protein was found at the Protein Data Bank's Molecule of the Month page for July 2004.

(Goodsell, David. Protein Data Bank Molecule of the Month: DNA Ligase. July 2004. http://www.pdb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb55_1.html)

 
DNA Ligase is composed of two domains with a deep gap between them. When crystallized with ATP, the binding site for this cofactor was found to be at the N-terminus of the larger domain, at the base of the cleft. DNA also binds in this cleft allowing for interaction between ATP and DNA to proceed. DNA Ligase is responsible for reconnecting DNA strands. This could mean the repair of damaged strands, or the connection of lagging strand Okazaki fragments in the process of DNA replication. Human DNA Ligase and the DNA Ligase from bacteriophage T7 use ATP as a cofactor. The reaction proceeds through the addition of AMP to the active site of the protein, and the release of pyrophosphate. AMP is then used to attach the 3' and 5' ends of a broken strand together.


DNA ligases in the repair and replication of DNA.

This review article focused on summarizing the function of DNA ligase proteins. These proteins catalyze the reaction of the joining of DNA fragments. Most forms of DNA ligase are found to be driven by ATP, but some bacteria use NAD(+) instead. The structure of the domain where adenylation occurs is surprisingly similar between these two different classes. This review went on to point out that multiple ligases are expressed in some organisms. DNA ligase I joins Okazaki fragments in DNA synthesis and does some repair work. DNA ligase III works in repain and recombination, and DNA ligase IV is necessary for joining non-homologous. This protein has many important functions! All of the ligases have a common structural core which is most likely similar to that of the bacteriophage T7.

(Timson, DJ. DNA ligases in the repair and replication of DNA. Mutat Res. 2000 Aug 30;460(3-4):301-18.)

Nick recognition by DNA ligases.

Although the mechanism by which DNA ligase catalyzes the repair of DNA fragments has been determined, the process by which breakages are recognized remains unknown. This article shows how bacteriophage T7 DNA ligase discriminates between breakages with either a 5’-phosphate or a 5’-OH.  This ligase prefers to bind to phosphorylated fragments to complete the sealing reaction. This T7 ligase works as a monomer with two very important residues, K238 and K240, which act in transadenylation and gap sealing. The cleft covers between 12 and 14 base pairs of DNA when in action.

(Doherty, AJ. Nick recognition by DNA ligases. J Mol Biol. 2000 Feb 11;296(1):43-56.)


Wednesday, March 2, 2011

DNA Ligase Pymol Representations

 Cartoon representation. Black background. Spectrum coloring.

Lines representation. White background. Spectrum coloring.

Cartoon representation. Light gray background. Prosthetic group in view. Colored by element. 

Ribbon representation. Black background. Spectrum coloring.
 
Surface view. Light gray background. Colored by secondary structure.
 

Ribbon representation. Black background. Associated with DNA.