Isomerase
In biochemistry, isomerases are a general class of enzymes that convert a molecule from one isomer to another. Isomerases facilitate intramolecular rearrangements in which bonds are broken and formed. The general form of such a reaction is as follows:
There is only one substrate yielding one product. This product has the same molecular formula as the substrate but differs in bond connectivity or spatial arrangement. Isomerases catalyze reactions across many biological processes, such as in glycolysis and carbohydrate metabolism.
Isomerization
Isomerases catalyze changes within one molecule. They convert one isomer to another, meaning that the end product has the same molecular formula but a different physical structure. Isomers themselves exist in many varieties but can generally be classified as structural isomers or stereoisomers. Structural isomers have a different ordering of bonds and/or different bond connectivity from one another, as in the case of hexane and its four other isomeric forms.Stereoisomers have the same ordering of individual bonds and the same connectivity but the three-dimensional arrangement of bonded atoms differ. For example, 2-butene exists in two isomeric forms: cis-2-butene and trans-2-butene. The sub-categories of isomerases containing racemases, epimerases and cis-trans isomers are examples of enzymes catalyzing the interconversion of stereoisomers. Intramolecular lyases, oxidoreductases and transferases catalyze the interconversion of structural isomers.
The prevalence of each isomer in nature depends in part on the isomerization energy, the difference in energy between isomers. Isomers close in energy can interconvert easily and are often seen in comparable proportions. The isomerization energy, for example, for converting from a stable cis isomer to the less stable trans isomer is greater than for the reverse reaction, explaining why in the absence of isomerases or an outside energy source such as ultraviolet radiation a given cis isomer tends to be present in greater amounts than the trans isomer. Isomerases can increase the reaction rate by lowering the isomerization energy.
Calculating isomerase kinetics from experimental data can be more difficult than for other enzymes because the use of product inhibition experiments is impractical. That is, isomerization is not an irreversible reaction since a reaction vessel will contain one substrate and one product so the typical simplified model for calculating reaction kinetics does not hold. There are also practical difficulties in determining the rate-determining step at high concentrations in a single isomerization. Instead, tracer perturbation can overcome these technical difficulties if there are two forms of the unbound enzyme. This technique uses isotope exchange to measure indirectly the interconversion of the free enzyme between its two forms. The radiolabeled substrate and product diffuse in a time-dependent manner. When the system reaches equilibrium the addition of unlabeled substrate perturbs or unbalances it. As equilibrium is established again, the radiolabeled substrate and product are tracked to determine energetic information.
The earliest use of this technique elucidated the kinetics and mechanism underlying the action of phosphoglucomutase, favoring the model of indirect transfer of phosphate with one intermediate and the direct transfer of glucose. This technique was then adopted to study the profile of proline racemase and its two states: the form which isomerizes L-proline and the other for D-proline. At high concentrations it was shown that the transition state in this interconversion is rate-limiting and that these enzyme forms may differ just in the protonation at the acidic and basic groups of the active site.
Nomenclature
Generally, "the names of isomerases are formed as "substrate isomerase", or as "substrate ''type of isomerase''"."Classification
Enzyme-catalyzed reactions each have a uniquely assigned classification number. Isomerase-catalyzed reactions have their own EC category: EC 5. Isomerases are further classified into six subclasses:Racemases, epimerases
This category includes. These isomerases invert stereochemistry at the target chiral carbon. Racemases act upon molecules with one chiral carbon for inversion of stereochemistry, whereas epimerases target molecules with multiple chiral carbons and act upon one of them. A molecule with only one chiral carbon has two enantiomeric forms, such as serine having the isoforms D-serine and L-serine differing only in the absolute configuration about the chiral carbon. A molecule with multiple chiral carbons has two forms at each chiral carbon. Isomerization at one chiral carbon of several yields epimers, which differ from one another in absolute configuration at just one chiral carbon. For example, D-glucose and D-mannose differ in configuration at just one chiral carbon. This class is further broken down by the group the enzyme acts upon:| EC number | Description | Examples |
| EC 5.1.1 | Acting on Amino Acids and Derivative | alanine racemase, methionine racemase |
| EC 5.1.2 | Acting on Hydroxy Acids and Derivatives | lactate racemase, tartrate epimerase |
| EC 5.1.3 | Acting on Carbohydrates and Derivatives | ribulose-phosphate 3-epimerase, UDP-glucose 4-epimerase |
| EC 5.1.99 | Acting on Other Compounds | methylmalonyl CoA epimerase, hydantoin racemase |
Cis-trans isomerases
This category includes enzymes that catalyze the isomerization of cis-trans isomers. Alkenes and cycloalkanes may have cis-trans stereoisomers. These isomers are not distinguished by absolute configuration but rather by the position of substituent groups relative to a plane of reference, as across a double bond or relative to a ring structure. Cis isomers have substituent groups on the same side and trans isomers have groups on opposite sides.This category is not broken down any further. All entries presently include:
| EC number | Examples |
| EC 5.2.1.1 | Maleate isomerase |
| EC 5.2.1.2 | Maleylacetoacetate isomerase |
| EC 5.2.1.4 | Maleylpyruvate isomerase |
| EC 5.2.1.5 | Linoleate isomerase |
| EC 5.2.1.6 | Furylfuramide isomerase |
| EC 5.2.1.8 | Peptidylprolyl isomerase |
| EC 5.2.1.9 | Farnesol 2-isomerase |
| EC 5.2.1.10 | 2-chloro-4-carboxymethylenebut-2-en-1,4-olide isomerase |
| EC 5.2.1.12 | Zeta-carotene isomerase |
| EC 5.2.1.13 | Prolycopene isomerase |
| EC 5.2.1.14 | Beta-carotene isomerase |
Intramolecular oxidoreductases
This category includes intramolecular oxidoreductases. These isomerases catalyze the transfer of electrons from one part of the molecule to another. In other words, they catalyze the oxidation of one part of the molecule and the concurrent reduction of another part. Sub-categories of this class are:| EC number | Description | Examples |
| EC 5.3.1 | Interconverting Aldoses and Ketoses | Triose-phosphate isomerase, Ribose-5-phosphate isomerase |
| EC 5.3.2 | Interconverting Keto- and Enol-Groups | Phenylpyruvate tautomerase, Oxaloacetate tautomerase |
| EC 5.3.3 | Transposing C=C Double Bonds | Steroid Delta-isomerase, L-dopachrome isomerase |
| EC 5.3.4 | Transposing S-S Bonds | Protein disulfide-isomerase |
| EC 5.3.99 | Other Intramolecular Oxidoreductases | Prostaglandin-D synthase, Allene-oxide cyclase |
Intramolecular transferases
This category includes intramolecular transferases. These isomerases catalyze the transfer of functional groups from one part of a molecule to another. Phosphotransferases were categorized as transferases with regeneration of donors until 1983. This sub-class can be broken down according to the functional group the enzyme transfers:| EC number | Description | Examples |
| EC 5.4.1 | Transferring Acyl Groups | Lysolecithin acylmutase, Precorrin-8X methylmutase |
| EC 5.4.2 | Phosphotransferases | Phosphoglucomutase, Phosphopentomutase |
| EC 5.4.3 | Transferring Amino Groups | Beta-lysine 5,6-aminomutase, Tyrosine 2,3-aminomutase |
| EC 5.4.4 | Transferring hydroxy groups | benzene mutase, Isochorismate synthase |
| EC 5.4.99 | Transferring Other Groups | Methylaspartate mutase, Chorismate mutase |
Intramolecular lyases
This category includes intramolecular lyases. These enzymes catalyze "reactions in which a group can be regarded as eliminated from one part of a molecule, leaving a double bond, while remaining covalently attached to the molecule." Some of these catalyzed reactions involve the breaking of a ring structure.This category is not broken down any further. All entries presently include:
| EC number | Examples |
| EC 5.5.1.1 | Muconate cycloisomerase |
| EC 5.5.1.2 | 3-carboxy-cis,cis-muconate cycloisomerase |
| EC 5.5.1.3 | Tetrahydroxypteridine cycloisomerase |
| EC 5.5.1.4 | Inositol-3-phosphate synthase |
| EC 5.5.1.5 | Carboxy-cis,cis-muconate cyclase |
| EC 5.5.1.6 | Chalcone isomerase |
| EC 5.5.1.7 | Chloromuconate cycloisomerase |
| EC 5.5.1.8 | -bornyl diphosphate synthase |
| EC 5.5.1.9 | Cycloeucalenol cycloisomerase |
| EC 5.5.1.10 | Alpha-pinene-oxide decyclase |
| EC 5.5.1.11 | Dichloromuconate cycloisomerase |
| EC 5.5.1.12 | Copalyl diphosphate synthase |
| EC 5.5.1.13 | Ent-copalyl diphosphate synthase |
| EC 5.5.1.14 | Syn-copalyl-diphosphate synthase |
| EC 5.5.1.15 | Terpentedienyl-diphosphate synthase |
| EC 5.5.1.16 | Halimadienyl-diphosphate synthase |
| EC 5.5.1.17 | -beta-macrocarpene synthase |
| EC 5.5.1.18 | Lycopene epsilon-cyclase |
| EC 5.5.1.19 | Lycopene beta-cyclase |
| EC 5.5.1.20 | Prosolanapyrone-III cycloisomerase |
| EC 5.5.1.n1 | D-ribose pyranase |