Ligase
Encyclopedia
In biochemistry
, ligase (from the Latin verb ligāre — "to bind" or "to glue together") is an enzyme
that can catalyse the joining of two large molecules by forming a new chemical bond
, usually with accompanying hydrolysis
of a small chemical group dependent to one of the larger molecules. In general, a ligase catalyzes the following reaction:
or sometimes
where the lowercase letters signify the small, dependent groups.
, an enzyme commonly used in molecular biology laboratories
to join together DNA
fragments. Other common names for ligases include synthetases, because they are used to synthesize
new molecules.
Note that, originally, biochemical nomenclature distinguished synthetases and synthase
s. Under the original 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 synthase is a lyase (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 synthetase is a ligase (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.
classification of enzymes. Ligases can be further classified into six subclasses:
Biochemistry
Biochemistry, sometimes called biological chemistry, is the study of chemical processes in living organisms, including, but not limited to, living matter. Biochemistry governs all living organisms and living processes...
, ligase (from the Latin verb ligāre — "to bind" or "to glue together") is an enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
that can catalyse the joining of two large molecules by forming a new chemical bond
Chemical bond
A chemical bond is an attraction between atoms that allows the formation of chemical substances that contain two or more atoms. The bond is caused by the electromagnetic force attraction between opposite charges, either between electrons and nuclei, or as the result of a dipole attraction...
, usually with accompanying hydrolysis
Hydrolysis
Hydrolysis is a chemical reaction during which molecules of water are split into hydrogen cations and hydroxide anions in the process of a chemical mechanism. It is the type of reaction that is used to break down certain polymers, especially those made by condensation polymerization...
of a small chemical group dependent to one of the larger molecules. In general, a ligase catalyzes the following reaction:
- Ab + C → A–C + b
or sometimes
- Ab + cD → A–D + b + c
where the lowercase letters signify the small, dependent groups.
Nomenclature
The common names of ligase enzymes often include the word "ligase," such as DNA ligaseDNA ligase
In molecular biology, DNA ligase is a specific type of enzyme, a ligase, that repairs single-stranded discontinuities in double stranded DNA molecules, in simple words strands that have double-strand break . Purified DNA ligase is used in gene cloning to join DNA molecules together...
, an enzyme commonly used in molecular biology laboratories
Laboratory
A laboratory is a facility that provides controlled conditions in which scientific research, experiments, and measurement may be performed. The title of laboratory is also used for certain other facilities where the processes or equipment used are similar to those in scientific laboratories...
to join together DNA
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
fragments. Other common names for ligases include synthetases, because they are used to synthesize
Biosynthesis
Biosynthesis is an enzyme-catalyzed process in cells of living organisms by which substrates are converted to more complex products. The biosynthesis process often consists of several enzymatic steps in which the product of one step is used as substrate in the following step...
new molecules.
Note that, originally, biochemical nomenclature distinguished synthetases and synthase
Synthase
In biochemistry, a synthase is an enzyme that catalyses a synthesis process.Following the EC number classification, they belong to the group of ligases, with lyases catalysing the reverse reaction....
s. Under the original 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 synthase is a lyase (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 synthetase is a ligase (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.
Classification
Ligases are classified as EC 6 in the EC numberEC number
The Enzyme Commission number is a numerical classification scheme for enzymes, based on the chemical reactions they catalyze....
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 synthetaseArgininosuccinate synthetaseArgininosuccinate synthase is an enzyme that catalyzes the synthesis of argininosuccinate from citrulline and aspartateASS is responsible for the third step of the urea cycle and one of the reactions of the Citrulline-NO cycle.-Gene:...
) - EC 6.4 includes ligases used to form carbon-carbon bonds
- EC 6.5 includes ligases used to form phosphoric ester bonds
- EC 6.6 includes ligases used to form nitrogen-metal bonds