Mechanistic Study of the Chlorella Virus DNA-Ligase by QM/MM Method

Abstract

DNA ligase is an enzyme which catalyzes the joining mechanism of single and double stranded breaks (Nicks) in DNA. They are required for DNA replication, repair and recombination. DNA ligase requires either ATP or NAD+ as the nucleotide cofactor. An overall mechanism of the enzyme was outlined based on the crystal structures of different DNA ligase enzymes at different steps. DNA ligation, joining of DNA strands, consists of three nucleotidyl transfer steps. The mechanism initiates with the formation of Ligase-AMP intermediate by the interaction of lysine from the active site of the enzyme with nucleotide cofactor (ATP or NAD+) in the step 1. In step 2, the formation of DNA-adenylate complex takes place through transferring the AMP nucleotide on 5’- phosphate group of the nicked DNA strand. This is followed by the formation of junction in phosphate backbone through attack of 3’-OH group on DNA-adenylate complex in step 3. These three steps are shown in Fig. 1.1 All three steps involve divalent metal ions. In this thesis, we have focused on the first step of the reaction. Using QM/MM based nudged elastic band calculation, we have explored various mechanisms and the minimum free energy path and the associate mechanisms.