DNA ligase is a protein that is used in both DNA repair and DNA replication (see Mammalian ligases). Furthermore, DNA ligase is often used in molecular biology laboratories for recombinant DNA research (see Research applications). Purified DNA ligase is used in gene cloning to link together DNA molecules to create recombinant DNA.
DNA ligase works by forming two covalent phosphodiester linkages between the 3′ hydroxyl ends of one nucleotide (“acceptor”) and the 5′ phosphate end of another (“donor”). For each phosphodiester bond produced, two ATP molecules are consumed. The ligase reaction requires AMP and happens in four steps:
Reorganisation of activity sites such as nicks in DNA segments or Okazaki fragments, among other things. Pyrophosphate is released as a result of adenylylation (the addition of AMP) of a lysine residue in the active core of the enzyme. Transfer of AMP to the so-called donor’s 5′ phosphate, creation of a pyrophosphate bond
A phosphodiester bond is formed between the donor’s 5′ phosphate and the acceptor’s 3′ hydroxyl.
Terminology
The DNA fragments, DNA segments, or Okazaki fragments are rearranged with their active sites in the first phase.
With the presence of AMP, the lysine residue of the Ligase’s active site is adenylated. Pyrophosphate is released as a result of Ligase adenylation.
Ligase catalyses the transfer of AMP to the donor’s 5′ phosphate end via the creation of a pyrophosphate bond.
The 5′ phosphate end of the donor forms a phosphodiester bond with the 3′ hydroxyl end of the receptor.
In general, these ligases are called after the substrate or macromolecules involved in the reaction; for example, amino acid–RNA ligase catalyses the creation of C-O bonds between amino acids and transfer RNA.
Characteristics of Ligase Enzymes
Ligase enzymes are the same as synthetase enzymes. Synthetase enzymes, on the other hand, are frequently mistaken with synthase enzymes. Historically, synthetase enzymes were defined as a “ligase that catalyses the joining of two macromolecules by utilising the energy molecules obtained by the hydrolysis of nucleoside triphosphates (such as ATP, GTP, CTP, TTP, and UTP), for example, the hydrolysis of adenosine triphosphate (ATP) molecules to adenosine diphosphate (ADP).”
Synthase enzymes, on the other hand, catalyse the synthesis of biological macromolecules without requiring the breakdown of nucleoside triphosphates.
However, the Joint Commission on Biochemical Nomenclature (JCBN) later announced that the terms synthetase and ligase will be used interchangeably. Simultaneously, the term synthase’ would be applied to synthesis-catalysing enzymes that may or may not include energy usage.
Ligases are one of six different types of enzymes. Oxidoreductases, transferases, hydrolases, isomerases, and lyases are some of the other enzyme classes. Ligase and lyase are enzyme classes that are closely linked. Ligase and lyase, on the other hand, are two separate types of enzymes.
Functions of ligase Enzymes
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DNA ligases are enzymes that seal breaks in the backbones of DNA, making them vital for all species’ existence
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DNA ligases have been researched from a variety of cells and creatures and have been found to have a wide range of sizes and sequences, with well conserved particular sequences essential for enzymatic activity
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We discuss the biochemical and structural characterization of a large number of DNA ligases that have been isolated or generated in recombinant forms
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Every DNA ligase has a crucial lysine that transfers an adenylate group from a cofactor to the 5′-phosphate of the DNA end, which will eventually be linked to the 3′-hydroxyl of the neighbouring DNA strand
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The cofactor for necessary DNA ligases in bacteria is -nicotinamide adenine dinucleotide (-NAD+), whereas the cofactor for essential DNA ligases in other organisms is adenosine-5′-triphosphate (ATP)
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This finding shows that the key bacterial enzyme could be targeted by new antibiotics, and the intricate molecular structure of -NAD+ allows for numerous chemical modifications
Conclusion
Several recent investigations have synthesised new derivatives, and their biological activity against a variety of DNA ligases has been assessed as drug discovery inhibitors and/or non-natural substrates for biochemical applications. We cover recent advances that signal new potential to modify the biochemical activity of these critical enzymes. The recent development of modified nucleotide derivatives demonstrates that the continuous combination of structural, biochemical, and biophysical approaches will be beneficial in targeting these key cellular enzymes.