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In biochemistry, a ligase is an enzyme that can catalyze the joining (ligation) of two molecules by forming a new chemical bond. This is typically via hydrolysis of a small pendant chemical group on one of the molecules, typically resulting in the formation of new C-O, C-S, or C-N bonds. For example, DNA ligase can join two complementary fragments of nucleic acid by forming phosphodiester bonds, and repair single stranded breaks that arise in double stranded DNA during replication.
In general, a ligase catalyzes the following dehydration reaction, thus joining molecules A and B:
A-OH + B-H → A–B + H2O
Nomenclature
editThe naming of ligases is inconsistent and so these enzymes are commonly known by several different names. Generally, the common names of ligases include the word "ligase", such as in DNA ligase, an enzyme commonly used in molecular biology laboratories to join together DNA fragments. However, many common names use the term "synthetase" or "synthase" instead, because they are used to synthesize new molecules[1]. There are also some ligases that use the name "carboxylase" to indicate that the enzyme specifically catalyzes a carboxylation reaction.
To note: biochemical nomenclature has sometimes distinguished synthetases from synthases and sometimes treated the words as synonyms[2]. Commonly, the two terms are used interchangeably and are both used to describe ligases.
Biochemical nomenclature has sometimes distinguished synthetases from synthases, but usually the terms are used interchangeably. Under one definition, synthases do not use energy from nucleoside triphosphates (such as ATP, GTP, CTP, TTP, and UTP), whereas synthetases do use nucleoside triphosphates. It is also said that a synthase is a lyase (a lyase is an enzyme that catalyzes the breaking of various chemical bonds by means other than hydrolysis and oxidation, often forming a new double bond or a new ring structure) and does not require any energy, whereas a synthetase is a ligase (a ligase is an enzyme that binds two chemicals or compounds) and thus requires energy. However, the Joint Commission on Biochemical Nomenclature (JCBN) dictates that "synthase" can be used with any enzyme that catalyses synthesis (whether or not it uses nucleoside triphosphates), whereas "synthetase" is to be used synonymously.[3]
^this section is plagiarized from https://www.axonmedchem.com/products/enzymes/ligases/synthetases#:~:text=Originally%2C%20biochemical%20nomenclature%20distinguished%20synthetases,synthetases%20do%20use%20nucleoside%20triphosphates.
Classification
editLigases are classified as EC 6 in the EC number classification of enzymes. Ligases can be further classified into six subclasses:
- EC 6.1 includes ligases used to form carbon-oxygen bonds
- EC 6.2 includes ligases used to form carbon-sulfur bonds
- EC 6.3 includes ligases used to form carbon-nitrogen bonds (including argininosuccinate synthetase)
- EC 6.4 includes ligases used to form carbon-carbon bonds, such as acetyl-CoA carboxylase
- EC 6.5 includes ligases used to form phosphoric ester bonds, such as DNA ligase
- EC 6.6 includes ligases used to form nitrogen-metal bonds, as in the chelatases
- ^ "IntEnz - EC 6". www.ebi.ac.uk. Retrieved May 2, 2023.
- ^ "Synthetases - Ligases - Enzymes - Products". www.axonmedchem.com. Retrieved May 2, 2023.
- ^ "Synthases and ligases". chem.qmul.ac.uk. Archived from the original on October 15, 2012. Retrieved July 28, 2013.