Structural Biochemistry/Enzyme Catalytic Mechanism/Enzyme Classification/Ligases

Overview

A ligase helps to form a bond between smaller molecules in order to form one large joined molecule by catalytic methods. This reaction usually involves the hydrolysis of a minor group branching off from one of the smaller molecules and usually needs ATPase, or some form of energy in order to carry out the reaction. This can be illustrated by the following reaction:

Aa + Bb --> Aa-B + b

Where [A] and [B] denote large molecules, [a] and [b] denote smaller molecules, and the dash [-] represents a new bond formed.

A page with a list of Ligases can be found here [[1]]

DNA ligase

DNA ligases are vital enzymes that function in important cellular processes, such as: DNA replication, repair of damaged DNA, and recombination. The enzyme forms phosphodiester bonds between adjacent 3'-OH and 5'-phosphate terminals to link the double stranded DNA. However, ligases may also repair and restore the nicks and cuts between double stranded DNA, double stranded RNA, or hybridized DNA/RNA strands.

Ligases can be classified into two groups depending on their requirement for ATP or NAD+ as the cofactor. All eukaryotic and viral enzymes require ATP, and most prokaryotic enzymes require NAD+ for their activity.

Ligase mechanism

Ligases are a type of enzyme that can catalyze ligation of two substrates through ATP hydrolysis. Ligases are seen in DNA and RNA ligation, where they bind two nucleotides by forming covalent phosphodiester bonds between 3'-OH ends of one nucleotide with the 5' phosphate end of another. The catalysis mechanism involves three steps:

1. The lysine residue of the enzyme is covalently linked to the adenylyl group from ATP and form an enzyme-AMP intermediate. The reaction is driven by the hydrolysis of the pyrophosphate in ATP. The ATP is the larger molecule in the graph shown below. 2. The adenynyl group of the enzyme-nucleotide intermediate is transferred to the 5’ phosphate group on the DNA strand. 3. The 3’-OH of the DNA strand attacks the phosphorus atom to displace the adenynyl group and form a phosphodiester bond in the DNA. By forming a pyrophosphate linkage and a good leaving group in the previous step, the 3’-OH of one nucleotide is readily bonded through nucleophilic attack.