Isomers present in many varieties can generally be divided into structural isomers and stereoisomers. Structural isomers have a different sequence and/or different connectivity of bonds from one another. Stereoisomers with the same ordering of individual bonds and the same connection type differ in the three-dimensional arrangement of bonded atoms. Intramolecular lyases, oxidoreductases and transferases in the sub-categories of isomerases catalyze the interconversion of structural isomers, while racemases, epimerases and cis-trans isomers promote the interconversion of stereoisomers. The prevalence of isomer in nature is partly dependent on the isomerization energy, the difference in inner energy between isomers. Isomers having similar energy levels can interconvert readily and are usually detected in comparable proportions. Isomerases can lower the isomerization energy and thus increase the reaction rate.

Classification

Isomerases have been assigned EC number of EC 5 and are further classified into six subclasses.

a. Racemases, epimerases

Isomerases in EC 5.1 include racemases and epimerases, both of which invert stereochemistry at the target chiral carbon. Racemases mainly act upon molecules with only one chiral carbon for stereochemical inversion, whereas epimerases target molecules with multiple chiral carbons by acting on one of them. Isomerization at one chiral carbon among several produces epimers, which differ from each other in absolute configuration at just one chiral carbon. This class is further divided according to the group the enzyme acts upon.

b. Cis-trans isomerases

Isomerases in EC 5.2 are enzymes that catalyze the isomerization of cis-trans isomers, which are not distinguished by absolute configuration but rather by the position of substituent groups with respect to a plane of reference, like a double bond or a ring structure. Molecules with substituents on the same side belong to cis isomers, while trans isomers have groups on opposite sides. This category contains entries as following.

c. Intramolecular oxidoreductases

Intramolecular oxidoreductases are categorized into EC 5.3 and they catalyze the transfer of electrons from one part of the molecule to another, meaning that the oxidation of one part of the molecule and the reduction of another part are concurrently catalyzed by this type of enzymes. Sub-categories of this class are listed below.

d. Intramolecular transferases

Intramolecular transferases (mutases) in EC 5.4 accelerate the transfer of functional groups from one part of a molecule to another. According to the functional groups the enzyme transfers, they can be further classified into five groups.

e. Intramolecular lyases

Isomerases in EC 5.5 are intramolecular lyases that catalyze reactions where a group can be regarded as eliminated from one part of a molecule, leaving a double bond, while keeping covalently attached to the molecule. Some of these types of reactions involve the destruction of a ring structure. This category cannot be further broken down and all entries presently are shown in the following table.

Mechanisms of Isomerases

Different types of isomerases have different action modes, mainly including ring expansion and contraction via tautomers, epimerization, intramolecular transfer, and intramolecular oxidoreduction.  

a. Ring expansion and contraction via tautomers

The isomerization of glucose (an aldehyde with a six-membered ring) to fructose (a ketone with a five-membered ring) is a classic example of ring opening and contraction catalyzed by an intramolecular oxidoreductase, glucose-6-phosphate isomerase, which involves the ring opening to form an aldose via acid/base catalysis and the formation of a cis-endiol intermediate. Subsequently, a protonated straight-chain ketose is formed and the ring is closed again.

b. Epimerization

The conversion of D-ribulose-5-phosphate into D-xylulose-5-phosphate in the Calvin cycle by ribulose-phosphate 3-epimerase belongs to epimerization, where the substrate and product differ only in stereochemistry at the third carbon in the chain. The deprotonation of that carbon to form a reactive enolate intermediate is likely to be an underlying mechanism, which presents a planar intermediate later gaining the opposite chirality from protonation on the other side. The alliance of these deprotonation-stabilization-protonation steps inverts the stereochemistry at the third carbon.

c. Intramolecular transfer

Chorismate mutase as an intramolecular transferase could catalyze the conversion of chorismate to prephenate that is employed as a precursor for L-tyrosine and L-phenylalanine in some plants and bacteria. This reaction belongs to a Claisen rearrangement that can proceed in the presence or absence of isomerase, and it passes through a chair transition state with the substrate at a trans-diaxial position. It has been indicated that the isomerase selectively binds to the chair transition state, and this binding could stabilize the transition state through electrostatic effects, which accounts for the sharp increase in the reaction rate with mutase or upon addition of a specifically-placed cation in the active site.

d. Intramolecular oxidoreduction

Isopentenyl-diphosphate delta isomerase type I (IPP isomerase) participates in the conversion of isopentenyl diphosphate (IPP) to dimethylallyl diphosphate (DMAPP) through stereoselective antarafacial transposition of a single proton, during which a stable carbon-carbon double bond is rearranged to leave a highly electrophilic allylic isomer. A tertiary carbocation intermediate at C3 is formed through the protonation of double bond at C4. Subsequently, the adjacent carbon, C2, is deprotonated from the opposite side to obtain a double bond. Indeed, the double bond gets shifted over.

Applications

Up to now, the application of isomerases in sugar manufacturing is the most common. Glucose isomerase catalyzes the transformation of D-glucose into D-fructose, which is a key part in high-fructose corn syrup production and results in a high yield of fructose with minimal side products. This enables a process more specific than older chemical methods for fructose production. Major concerns of the utilization of glucose isomerase are caused by its inactivation at higher temperatures and requirement for high pH during the reaction. The optimum activity of this enzyme can be achieved only with the presence of a divalent cation such as Co²⁺ or Mg²⁺, at an additional cost to manufacturers. A much higher affinity for xylose than for glucose of the enzyme also necessitates a carefully controlled environment.

The efficient isomerization of xylose to xylulose by glucose isomerase is found naturally in bacteria that feed on decaying plant matter. Commercial values have been demonstrated through the production of ethanol, achieved by the fermentation of xylulose. Glucose isomerase is also capable of speeding isomerization of a range of other sugars, including D-ribose, D-allose and L-arabinose. The current mechanism model of glucose isomerase is a hydride shift, as revealed by isotope exchange and X-ray crystallography studies. Overall, extensive research in genetic engineering has been focused on the optimization and recovery of glucose isomerase from industrial processes for reuse.

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Isomerases