In
biochemistry
Biochemistry, or biological chemistry, is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology, a ...
, a ligase is an
enzyme
An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...
that can
catalyze
Catalysis () is the increase in rate of a chemical reaction due to an added substance known as a catalyst (). Catalysts are not consumed by the reaction and remain unchanged after it. If the reaction is rapid and the catalyst recycles quick ...
the joining (
ligation) of two molecules by forming a new
chemical bond
A chemical bond is the association of atoms or ions to form molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds or through the sharing of electrons a ...
. This is typically via
hydrolysis
Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution reaction, substitution, elimination reaction, elimination, and solvation reactions in which water ...
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
DNA ligase is a type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such ...
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 + H
2O
Nomenclature
The 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
DNA ligase is a type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such ...
, an enzyme commonly used in molecular biology
laboratories
A laboratory (; ; colloquially lab) is a facility that provides controlled conditions in which science, scientific or technological research, experiments, and measurement may be performed. Laboratories are found in a variety of settings such as s ...
to join together
DNA
Deoxyribonucleic acid (; DNA) is a polymer composed of two polynucleotide chains that coil around each other to form a double helix. The polymer carries genetic instructions for the development, functioning, growth and reproduction of al ...
fragments. However, many common names use the term "synthetase" or "synthase" instead, because they are used to
synthesize new molecules. There are also some ligases that use the name "carboxylase" to indicate that the enzyme specifically catalyzes a
carboxylation
Carboxylation is a chemical reaction in which a carboxylic acid is produced by treating a substrate with carbon dioxide. The opposite reaction is decarboxylation. In chemistry, the term carbonation is sometimes used synonymously with carboxylation ...
reaction.
To note: biochemical nomenclature has sometimes distinguished synthetases from
synthases and sometimes treated the words as
synonym
A synonym is a word, morpheme, or phrase that means precisely or nearly the same as another word, morpheme, or phrase in a given language. For example, in the English language, the words ''begin'', ''start'', ''commence'', and ''initiate'' are a ...
s. Commonly, the two terms are used interchangeably and are both used to describe ligases.
Classification
Ligases 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
This list contains a list of Enzyme Commission number, EC numbers for the sixth group, EC 6, ligases, placed in numerical order as determined by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology. All offici ...
includes ligases used to form carbon-nitrogen bonds (including
argininosuccinate synthetase
Argininosuccinate synthase or synthetase (ASS; ) is an enzyme that catalyzes the synthesis of argininosuccinic acid, argininosuccinate from citrulline and aspartic acid, aspartate. In humans, argininosuccinate synthase is encoded by the ''ASS ...
)
*
EC 6.4 includes ligases used to form carbon-carbon bonds, such as
acetyl-CoA carboxylase
Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme () that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT). ACC ...
*
EC 6.5 includes ligases used to form
phosphoric ester bonds, such as
DNA ligase
DNA ligase is a type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such ...
*
EC 6.6 includes ligases used to form nitrogen-metal bonds, as in the
chelatases
Membrane-associated ligases
Some ligases associate with
biological membranes as
peripheral membrane protein
Peripheral membrane proteins, or extrinsic membrane proteins, are membrane proteins that adhere only temporarily to the biological membrane with which they are associated. These proteins attach to integral membrane proteins, or penetrate the periph ...
s or anchored through a single
transmembrane helix,
Superfamilies of single-pass transmembrane ligases
in Membranome database for example certain ubiquitin ligase
A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin ...
related proteins.
Etymology and pronunciation
The word ''ligase'' uses combining forms of '' lig-'' (from the Latin
Latin ( or ) is a classical language belonging to the Italic languages, Italic branch of the Indo-European languages. Latin was originally spoken by the Latins (Italic tribe), Latins in Latium (now known as Lazio), the lower Tiber area aroun ...
verb ''ligāre'', "to bind" or "to tie together") + ''-ase
The suffix -ase is used in biochemistry to form names of enzymes. The most common way to name enzymes is to add this suffix onto the end of the substrate, ''e.g.'' an enzyme that breaks down peroxides may be called peroxidase; the enzyme that pr ...
'' (denoting an enzyme), yielding "binding enzyme".
See also
*DNA ligase
DNA ligase is a type of enzyme that facilitates the joining of DNA strands together by catalyzing the formation of a phosphodiester bond. It plays a role in repairing single-strand breaks in duplex DNA in living organisms, but some forms (such ...
*Acetyl-CoA carboxylase
Acetyl-CoA carboxylase (ACC) is a biotin-dependent enzyme () that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT). ACC ...
*Nuclease
In biochemistry, a nuclease (also archaically known as nucleodepolymerase or polynucleotidase) is an enzyme capable of cleaving the phosphodiester bonds that link nucleotides together to form nucleic acids. Nucleases variously affect single and ...
*Protease
A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalysis, catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products ...
*Ubiquitin ligase
A ubiquitin ligase (also called an E3 ubiquitin ligase) is a protein that recruits an E2 ubiquitin-conjugating enzyme that has been loaded with ubiquitin, recognizes a protein substrate, and assists or directly catalyzes the transfer of ubiquitin ...
References
EC 6 Introduction
from the Department of Chemistry at Queen Mary, University of London
Queen Mary University of London (QMUL, or informally QM, and formerly Queen Mary and Westfield College) is a public research university in Mile End, East London, England. It is a member institution of the federal University of London.
Today, ...
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