DNA Ligase

^[1]

Structure and Function

The Crystal Structure:

 ^[2][3]

DNA ligase has many unique features.  DNA ligase is a monomer and vital enzyme that was first discovered in 1967 by scientists in different laboratories around the same time (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=stryer.section.3794#3800).  The two domains that make up the crystal structure are the C-termainal domain, and the N-terminal domain, which is larger (http://sci.cancerresearchuk.org/labs/wigley/projects/ligase/ligase.html).  DNA ligase depends on a cofactor molecule, usually ATP (NAD in some bacteria) for energy and uses a lysine amino acid to carry out the reaction (http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb55_1.html).  DNA ligase repairs breaks in double stranded DNA by forming a phosphodiester bond between the 3'-hydroxyl end of one fragment to the 5'-phosphate end of the other fragment (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=stryer.section.3794#3800).  The ATP gives the ligase its active AMP which forms a complex with the lysine, causing the 3' end to carry out a neucleophilic attack on the 5' end (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=stryer.section.3794#3800).  The ligation reaction proceedes as follows: ^[4]

 Mechanisms

1. DNA Replication:         

     DNA Ligase is used at the final stage of DNA replication to join the 3'-hydroxyl end of one Okazaki fragment to the 5'-phosphate end of the adjacent fragment (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.figgrp.3196).  Throughout replication the Okazaki fragments are covalently attatched by DNA ligase(http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=stryer.section.3794#3800).During the ligation the DNA ligase temporarily connects to the 5'-phosphate group of one DNA strand, which activates the phosphate group(http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.figgrp.3196).  The ligase then joins the adjacent completed Okazaki fragments(http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=mcb.section.3186#3195).

2. DNA Repair:

     After DNA has been damaged and has unwound near the damaged site and a particular repair system has done its job, the gaps will be filled in using DNA polymerase I, and the nick is sealed by DNA ligase (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mcb.figgrp.3252).

     Types of repair systems used:

• Mismatch Repair
• Base Excision Repair
• Nucleotide Excision Repair
• Double-Strand Break Repair

3. DNA Recombination:

     The recombination process is completed using DNA ligase to reseal the DNA fragments (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=mboc4.section.870#875).

     DNA ligase has also become important in recombinant DNA technology, DNA cloning with plasma vectors, and gene replacement.

Association with Human Diseases

     The DNA repair mechanisms that DNA ligase is a part of are sometimes nonfunctioning or error-producing can lead to mutations (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=mcb.section.3235#3256).  This is the reason DNA damage from radiation or chemical carcinogens cause tumors to form (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=mcb.section.3235#3256).  So, processes that reapair DNA are thought to both protect and contribute to cancer development (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=mcb.section.3235#3256).  There are certain cytotoxic anticancer drugs that are used to target certain enzymes that are used for different cellular processes (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=cmed6.section.11071#11075).  For example, the triphosphate of fludarabine incorporates itself into DNA, and inhibits the function of DNA ligase, among others (http://www.ncbi.nlm.nih.gov/books/bv.fcgi?highlight=DNA%20ligase&rid=cmed6.section.11071#11075).