In biochemistry, ligase, also called synthetase, is an enzyme catalyzing the joining of two large molecules through the formation of a new chemical bond such as C-O, C-S, C-N, or the linking together of two compounds, usually accompanied with the hydrolysis of a small attached chemical group to one of the larger molecules. This procedure usually assimilates the needed energy from the cleavage of an energy-rich phosphate bond, involves the conservation of chemical energy and offers a linkage between energy-requiring synthetic processes and energy-yielding breakdown reactions. In most cases, the simultaneous conversion of ATP to adenosine ADP functions as a source of energy. The ligase catalyzed reaction has a general formulation as following:

Nomenclature

The common names of ligases often contain the word "ligase", like DNA ligase, a frequently used enzyme in molecular biolaboratory to link DNA fragments together. Synthetase is another commonly adopted name for ligases since they are applied in the synthesis of new molecules. Synthetases sometimes are distinguished from synthases and sometimes treated as synonym of synthases. From the view of definition, nucleoside triphosphates such as ATP, GTP, CTP, TTP, and UTP, are employed by synthetases to produce energy, whereas synthases do not use nucleoside triphosphates. A synthase is also acknowledged as a lyase that catalyzes the cleavage of various chemical bonds through means excluding hydrolysis and oxidation without demand for any energy, whereas a synthetase is a ligase joining two chemicals or compounds with requirement for energy. The Joint Commission on Biochemical Nomenclature (JCBN) has dictated that synthase can represent any enzyme that catalyzes synthesis, while synthetase needs to be used synonymously.

Classification

In the EC number classification system, ligases are classified as EC 6 and can be further classified into six subclasses.

Applications of Several Common Ligases

DNA ligase is a specific type of enzyme that promotes the joining of DNA strands together by catalyzing the formation of a phosphodiester bond between phosphate and deoxyribose. DNA ligase is active during the replication, repair and recombination process of DNA. It is widely applied in the repair of single-strand breaks in duplex DNA of living organisms using the complementary strand of the double helix as a template, while some forms may specifically mend double-strand damages. In molecular biology laboratories, purified DNA ligase is extensively used in gene cloning to join DNA molecules together to form recombinant DNA. Another innovative application of DNA ligase can be seen in nano chemistry field, particularly in DNA origami. DNA ligase can offer enzymatic assistance that is essential to construct DNA lattice structure from DNA over hangs, thus further assembling nanoscale objects, like nanomachines, nanoelectronic, biomolecules, and photonic component.

As another typical example of ligase, T4 RNA ligase 1 is capable of catalyzing the ATP-dependent covalent joining of single-stranded 5'-phosphoryl termini of RNA to single-stranded 3'-hydroxyl termini of RNA. T4 RNA ligase 2 is distinguished by critical signature residues and a unique C-terminal domain that is essential for sealing of 3'-OH and 5'-phosphoryl RNA ends and also catalyzes the joining of a 3'-hydroxyl end of RNA to a 5'-phosphorylated RNA. Unlike T4 RNA ligase 1, it prefers double-stranded substrates and a pre-adenylated substrate is required in ligation by a truncated form of T4 RNA ligase 2. T4 RNA ligase is able to label RNA 3'-end with cytidine 3',5'-bis [α-32P] phosphate, induce the circularization of synthetic oligonucleotides, and site-specificly generate composite primers for PCR. Specific modifications of tRNAs could also be accomplished under the assistance of T4 RNA ligase, which also catalyzed the ligation of oligodeoxyribonucleotide to single-stranded cDNAs for 5'-RACE.

Ubiquitin ligase, also called an E3 ubiquitin ligase, is an enzyme existing as a single polypeptide or a multimeric complex. E3 Ubiquitin ligase could work together with ubiquitin activating enzyme E1 and ubiquitin conjugating enzyme E2 that has been loaded with ubiquitin, to accelerate the ubiquitination of various protein substrates for targeted degradation by proteasome. The ubiquitin is ultimately attached to a lysine on the substrate protein though an isopeptide bond and E3 ligases could interact with both the target protein and the E2 enzyme, thus imparting substrate specificity to E2 enzyme. Ubiquitination by E3 ubiqutin ligases also plays an essential role in regulation of many biological processes, such as cell trafficking, DNA repair, and signaling. It is of profound importance in cell biology. E3 ligases also occupy a position in cell cycle control and the degradation of cyclins. The human genome encodes more than 600 putative E3 ligases, resulting in tremendous diversity in substrates, while E3s could determine the specificity of protein substrates. Recent research has found that many E3s have been implicated in human disease and they are a class of attractive “drugable” targets for pharmaceutical intervention.

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Ligases