Enzyme Definition and Classification - Technology Networks

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Enzyme Definition and Classification


Ligases

Oxidoreductases

Transferases

Isomerases Hydrolases

Lyases

Definition Classification

An enzyme is a protein or RNA produced by living cells, which is highly specific and highly catalytic to its substrates.

Enzymes are a very important t y p e o f m a c r o m o l e c u l a r biological catalysts.


EC 1 Oxidoreductases Catalyze the transfer of electrons from an electron donor to an

electron acceptor molecule

A is the reductant and B is the oxidant


Classification

EC number Description EC number Description

EC 1.1 Act on the CH-OH group of donors EC 1.12 Act on hydrogen as donors

EC 1.2 Act on the aldehyde or oxo group of donors EC 1.13 Act on single donors with incorporation of molecular oxygen

EC 1.3 Function on the CH-CH group of donors EC 1.14 Function on paired donors with incorporation of oxygen

EC 1.4 Functioning on the CH-NH2 group of donors EC 1.15 Act on and act on superoxide radicals as acceptors

EC 1.5 Act on CH-NH group of donors EC 1.16 Oxidize metal ions

EC 1.6 Act on NADH or NADPH EC 1.17 Take effect on CH or CH2 groups

EC 1.7 Take other nitrogenous compounds as donors EC 1.18 Apply iron-sulfur proteins as donors

EC 1.8 Act on a sulfur group of donors EC 1.19 Take reduced flavodoxin as donors

EC 1.9 Act on a heme group of donors, respectively EC 1.20 Dispose phosphorus or arsenic in donors

EC 1.10 Treating diphenols and related substances as donors EC 1.21 Form a X-Y bond from X-H and Y-H bond

EC 1.11 Act on peroxide as an acceptor (peroxidases) EC 1.97 Some other oxidoreductases

Oxidoreductases are sorted as EC 1 in the EC number classification of enzymes and can be further classified into 22 subclasses


Functions

Accelerate the reduction of NAD+ to NADH

GlycolysisThe glycolysis product pyruvate takes part in the TCA cycle in a form of acetyl-CoA.

TCA cycle

Oxidization of the generated NADH to NAD+ occurs to maintain the redox state of the cell

Oxidative phosphorylation All twenty of the amino acids, except for leucine and lysine, can be degraded to intermediates

Amino acid metabolism


EC 2 Transferases Transfer specific functional groups from one molecule (donor) to

another (acceptor)

X is the donor that is often a coenzyme, and Y is the acceptor


In 1930s, some of the most important transferases were discovered.

Systematic names of transferases are based on the form of "donor:acceptor grouptransferase."

The more frequently used nomenclature for transferases are often in a form of "acceptor grouptransferase" or "donor grouptransferase."

Practically, many molecules are not mentioned by taking advantage of this terminology because of the application of more prevalent common names.

Later in 1953, enzyme UDP-glucose pyrophosphorylase was revealed to be a transferase.

In 1970, the breakdown mechanism of catecholamine by catechol-O-methyltransferase was illuminated.


Classification

EC 2.1 Transfer single-carbon groups

EC 2.3 Transfer acyl groups

EC 2.4 Transfer glycosyl, hexosyl and pentosyl groups

EC 2.2 Transfer aldehyde or ketone groups

EC 2.5 Transfer alkyl or aryl groups

EC 2.9 Selenium transferases

EC 2.6 Transfer nitrogenous groups

EC 2.7 Transfer phosphorus-containing groups

EC 2.8 Transfer sulfur-containing groups

EC 2.10 Transfer molybdenum or tungsten-containing groups

Transferases have been assigned a number of EC 2 in the EC numbering system and contain ten subclassses


Applications in Biotechnology

Terminal transferase could label DNA or produce plasmid vectors by adding deoxynucleotides

Glutathione transferases could also increase resistance to both biotic and abiotic stress in transgenic plants. They are being explored as targets for anti-cancer medications owing to their functionality in drug resistance.

Glutathione transferases can be applied by plants to segregate toxic metals from the rest of the cell, which

thus can be processed as biosensors to detect contaminants such as herbicides and insecticides.


EC 3 Hydrolases Utilize water to break a chemical bond in order to divide a large

molecule into two smaller molecules


Classification

Hydrolases belongs to EC 3 in the EC classification system and can be further grouped into thirteen subclasses


Functions

Stimulate liver to secrete bile salts which facilitate the

digestion of food

Increase hydrogel-forming potencies of

certain bile salts

Serves as guidance in the development of new medicines for the prevention and treatment of gastrointestinal disorders

As biomarker for low dose exposure to

organophosphorus in humans

Significant in various biological processes like the metabolism of cell

wall, the biosynthesis of glycans, signalling, plant defence

As a bifunctional zinc metalloenzyme in the 5-lioxygenase pathway and

possesses a peptide-cleaving activity


EC 4 Lyases Catalytically break various chemical bonds by means of an

"elimination" reaction, other than hydrolysis and oxidation


Classification

Cleave carbon-carbon bondsEC 4.1

Break carbon-oxygen bondsEC 4.2

Cleave carbon-nitrogen bonds 3EC 4.3

Cleave carbon-sulfur bonds4EC 4.4

Cleave carbon-halide bonds EC 4.5

Break phosphorus-oxygen bondsEC 4.6

A group of other lyases3EC 4.7

EC 4: Lyases


Substrate Specificity & Cofactor Requirements

Most lyases require cofactors

Substrate Specificity

Narrow substrate specificity

Depend on its source

Not an absolute prerequisite

Not very expensiveCofactor Requirements

Bound to the enzyme


EC 5 Isomerases Convert a molecule from one isomer to another


Classification

EC 5IsomerasesEpimerases

Racemases

Cis-trans isomerases

Intramolecular transferases

Intramolecular oxidoreductases

Intramolecular lyases


Isomerization

Isomers

Structural Isomers

Stereoisomers

IntramolecularLyases

Cis-trans Isomers Racemases

Epimerases Oxidoreductases

Transferases

Catalyze Catalyze


EC 6 Ligases Catalyze the joining of two large molecules through the formation of

a new chemical bond


Nomenclature

ClassificationEC number DescriptionEC 6.1 Form carbon-oxygen bondsEC 6.2 Form carbon-sulfur bondsEC 6.3 Form carbon-nitrogen bonds (Argininosuccinate synthetase)EC 6.4 Form carbon-carbon bondsEC 6.5 Form phosphoric ester bondsEC 6.6 Form nitrogen-metal bonds, as in the chelatases

The common names of ligases often contain

the word “ligase”.

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.


Catalyze the formation of a phosphodiester bond between phosphate and deoxyribose

Typical Examples

Active during the replication, repair and recombination process of DNA

Employed in gene cloning to join DNA molecules together to form recombinant DNA

Catalyze the ATP-dependent covalent joining of single-stranded 5'-phosphoryl termini to single-stranded 3'-hydroxyl termini of RNA

Label RNA 3'-end with cytidine 3',5'-bis [α-32P] phosphate

Generate composite primers for PCR and specificly modify tRNAs

Induce the circularization of synthetic oligonucleotides

Catalyze the ligation of oligodeoxyribonucleotide to single-stranded cDNAs for 5'-RACE

Accelerate the ubiquitination of various protein substrates for targeted degradation by proteasome

Play an essential role in regulation of many biological processes

Control cell cycle and degrade cyclins

Determine the specificity of protein substrates

A class of attractive “drugable” targets for pharmaceutical intervention

DNA ligase

RNA ligase

Ubiquitin ligase


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Enzyme Definition and Classification - Technology Networks