Friday, April 22, 2011

DNA Ligase

DNA--- the information-holding material of the cell which had scientists stumped for decades. Is it possible that something that seems so simple can hold the extensive information needed for a cell to function? How can a pattern of A, C, T, and G encode the various specialized proteins necessary for advanced life to occur? How is this “knowledge” passed on from the mother cell to the daughter cells?
The mechanism of the method of genetic inheritance, was one that obligated the careers of many scientists. The process of DNA replication is thought to be quite well known today as a result of their work.
Needless to say, the process of DNA synthesis is absolutely essential during cell proliferation as seen in reproduction and growth. DNA Ligase is a protein which functions during the replication process of DNA to ensure that the complementary, double-stranded structure of DNA results. DNA Ligase functions in piecing together the Okazaki fragments of the lagging strand to form a continuous complementary strand. The reaction it catalyzes requires the use of ATP. AMP is added to the active site releasing pyrophosphate. DNA then enters the active site and the AMP is used to attach together the 3’ and 5’ ends of the lagging strand.
DNA Ligase interacting with ATP
Not only is DNA Ligase in action during DNA synthesis, but also during DNA repair. Some harsh environmental or intracellular factors, such as UV radiation or radicals, can cause breaks in the DNA chain requiring DNA Ligase activity. The structure of DNA Ligase facilitates its ability to recognize the damage and catalyze the crucial reactions to repair our information source. The enzyme is composed of two domains with a deep gap between them where both DNA and ATP are bound. Upon the binding of DNA and ATP, pyrophosphate is released, and the strand is returned to its former, continuous state.  
        If not for DNA Ligase, genetic information would not be able to be passed from mother to daughter cell, and each event resulting in the breakage of a DNA strand would result in malfunction and potentially cell death.

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.

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.