3. ISOMEARASE
■ 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.
■ Isomerases belong to the EC 5 primary class of enzymes that catalyze the reactions involving
a structural rearrangement of a molecule.
■ The general form of such a reaction is as follows:
■ They convert one isomer to another, meaning that the end product has the same molecular
formula but a different physical structure.
■ There is only one substrate yielding one product.
https://en.wikipedia.org/wiki/Isomerase
https://www.qmul.ac.uk/sbcs/iubmb/enzyme/rules.html
4. ■ Isomerases are important biological components of the metabolism and genome
of most living organisms.
■ All isomerases have Enzyme Commission numbers beginning in EC 5.
■ Isomerases catalyze reactions across many biological processes, such as in
glycolysis and carbohydrate metabolism.
■ According to the type of isomerism, they may be called racemases, epimerases,
cis-trans-isomerases, isomerases, tautomerases, mutases or cycloisomerases.
Some Examples:
• Glucose isomerse
• diphosphoglycerate
mutase
• photo isomerase.
• Maleate isomerase
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4139
412/
6. Racemases, epimerases
■ These isomerases invert stereochemistry at the target chiral carbon.
■ Racemases act upon molecules with one chiral carbon whereas epimerases target molecules
with multiple chiral carbons.
■ This class is further broken down by the group the enzyme acts upon:
■ This class is further broken down by the group the enzyme acts upon:
■ https://en.wikipedia.org/wiki/Isomerase
■ https://en.wikipedia.org/wiki/Isomerase
EC number Description Examples
EC 5.1.1
Acting on Amino Acids and
Derivative
alanine racemase, methionine
racemase etc.
EC 5.1.2
Acting on Hydroxy Acids and
Derivatives
lactate racemase, tartrate
epimerase etc.
EC 5.1.3
Acting on Carbohydrates and
Derivatives
ribulose-phosphate 3-epimerase,
UDP-glucose 4-epimerase etc.
EC 5.1.99 Acting on Other Compounds
methylmalonyl CoA epimerase,
hydantoin racemase etc.
https://en.wikipedia.org/wiki/Isomerase
7. Acting on Amino Acids and
Derivative
Acting on Hydroxy Acids and
Derivatives
EC 5.1.1.1
Accepted name: alanine racemase
Reaction: L-alanine = D-alanine
Other name(s): L-alanine racemase
Systematic name: alanine racemase D- alanine L- alanine
EC 5.1.2.1
Accepted name: lactate racemase
Reaction: (S)-lactate = (R)-lactate
Other name(s): lactico racemase; hydroxyacid
racemase; lactic acid racemase
Systematic name: lactate racemase
Acting on Carbohydrates and
Derivatives
Acting on Other Compounds
EC 5.1.3.1
Accepted name: ribulose-phosphate 3-epimerase
Reaction: D-ribulose 5-phosphate = D-xylulose 5-
phosphate
Other name(s): phosphoribulose epimerase;
erythrose-4-phosphate isomerase; pentose-5-
phosphate 3-epimerase
Systematic name: D-ribulose-5-phosphate 3-
EC 5.1.99.1
Accepted name: methyl malonyl-CoA epimerase
Reaction: (R)-methyl malonyl-CoA = (S)-methyl
malonyl-CoA
Other name(s): methyl malonyl-CoA racemase; methyl
malonyl coenzyme A racemase; DL-methyl malonyl-
CoA racemase
Systematic name: methyl malonyl-CoA 2-epimerase
https://www.enzyme-database.org
8. ■ CIS-TRANS ISOMERISM
Also known as geometric isomerism or configurational isomerism.
Cis- functional groups are on the same side of the carbon chain.
Trans- functional groups are on opposing sides of the carbon chain.
https://en.wikipedia.org/wiki/Cis%E2%80%93trans_isomerism
9. Cis-Trans Isomerases
■ cis-trans isomerase is a type of isomerase which catalyzes the isomerization of
geometric isomers.
Example- 1.Photoisomerase- group of enzymes that catalyze the isomerization of
photopigments.
Rhodopsin is a pigment present in rods of retina. A retinal isomerase is an enzyme
that catalyzes the isomerization of trans retinal in eye into 11-cis-retinal which is
form suitable to bind with protein opsin.
2.Immunophilins are cellular proteins that display a peptidylprolyl cis–trans
isomerase (PPI'ase) enzymatic activity.
3.Cyclophilins are an immunosuppressant which is usually used to suppress
rejection after internal organ transplants. These proteins catalyzes the
isomerization of peptide bonds from trans form to cis form at proline residues.
https://pubmed.ncbi.nlm.nih.gov/1403367/
10. ■ INTRAMOLECULAR OXIDOREDUCTASES
Enzymes of the isomerase class that catalyze the oxidation of one part of a molecule
with a corresponding reduction of another part of the same molecule.
Examples: Aldose-Ketose Isomerases; Carbon-Carbon Double Bond Isomerases;
Sulfur-Sulfur Bond Isomerases.
1.Aldose-Ketose isomerases- Enzymes that catalyze the interconversion of aldose
and ketose compounds EC 5.3.1
Example- Ribose 5 phosphate isomerase- catalyzes the conversion between ribose-
5- phosphate to ribulose- 5- phosphate. Role in calvin cycle and carbohydrate
metabolism.
http://www.reference.md/files/D019/mD019746.html#:~:text=Definition%3A
%20Enzymes%20of%20the%20isomerase,part%20of%20the%20same%2
0molecule.
11. 2. Carbon carbon double bond isomerase- Enzymes that catalyze the shifting of a carbon-carbon
double bond from one position to another within the same molecule. EC 5.3.3.
Example- L-dopachrome isomerase- This enzyme participates in melanogenesis.
3.Sulphur sulphur bond isomerase- Enzymes that catalyze the transposition of a sulfur-sulfur bond.
EC 5.3.4.
Example- Protein Disulfide-Isomerases- Catalyze the rearrangement of disulfide
bonds within proteins during folding. Present in endoplasmic reticulum in
eukaryotes and the periplasm of bacteria that catalyzes the formation and breakage
of disulfide bonds between cysteine residues within proteins as they fold.
4.Keto-enol isomerase- Interconversion of keto and enol forms .EC 5.3.2
Example- Oxaloacetate tautomerase- keto-oxaloacetate enol-oxaloacetate.
12. INTRAMOLECULAR TRANSFERASES
■ Enzymes of the isomerase class that catalyze the transfer of acyl-phospho- amino or other groups
from one position with in a molecule to another.
EXAMPLES: Methylmalonyl-CoA mutase; benzene mutase; phosphogluco mutase;
phosphoenolpyruvate mutase; phosphoenolglycerate mutase.
1.Metylmalonyl-CoA mutase – MCM was first identified in rat liver or sheep kidney in 1955. It is a
protein that in humans is encoded by MUT gene. This enzyme catalyse the isomerisation of
methylmalonyl-CoA to succinyl –CoA, requiring cobalamine in the form of adenosylcobalamine as a
cofactor. This reaction is required for the degradation of odd chain fatty chain.
The substrate of methymalonyl-CoA mutase, is primerly derived from propionyl-CoA, a substance
formed from the catabolism and digestion of valine, threonine, methionine, thymine etc. and the
product of enzyme succiyl-CoA.
13. 2. Phosphoglucomutase – It is an enzyme that transfers a phosphate group on an α- D – glucose
monomer from the one 1 to 6 position in the forward direction or the 6 to 1 position the reverse
direction .
■ Role in glycogenesis
Phosphoglucomutase also acts in the opposite fashion when blood glucose levels are high. In
this case, phosphoglucomutase catalyzes the conversion of glucose 6-phosphate (which is
easily generated from glucose by the action of hexokinase) to glucose 1-phosphate.
14. 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.
Examples:
■ Muconate cycloisomerase : Muconate lactonizing enzymes are involved in the breakdown
of lignin-derived aromatics, catechol and protocatechuate, to citric acid cycle intermediates as a
part of the β-ketoadipate pathway in soil microbes. The structure of the Muconate lactonizing
enzymes (MLEs) consists of a seven-bladed beta propeller with various modifications based on
the type of class that it belongs to. MLEs catalyze the bacterial β-ketoadipate pathways by
catabolizing aromatic lignin found in plants to intermediates found in the Krebs Cycle. Some
MLEs can be halogenated with Cl and perform slightly different functions in the microbe.
Halogenated MLEs can remove Cl from halogenated aromatics allowing for the decomposition of
2,4-dichlorophenoxyacetate.
15. 2. Inositol-3-phosphate synthase
This enzyme belongs to name of this enzyme class is 1D-myo-inositol-3-phosphate of the family
of isomerases, specifically the class of intramolecular lyases. The systematic lyase (isomerizing).
Other names in common use include myo-inositol-1-phosphate synthase, D-glucose 6-
phosphate cycloaldolase, inositol 1-phosphate synthetase, glucose 6-phosphate
cyclase, inositol 1-phosphate synthetase, glucose-6-phosphate inositol monophosphate
cycloaldolase, glucocycloaldolase, and 1L-myo-inositol-1-phosphate lyase (isomerizing).
16. MECHANISMS OF ISOMERASES
Different types of isomerases have different action modes such as:
■ 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.
https://www.creative-enzymes.com/resource/isomerase-
introduction_23.html
17. ■ 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.
https://www.creative-enzymes.com/resource/isomerase-
introduction_23.html
18. ■ 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. Experimental evidence indicates that the isomerase selectively binds
the chair transition state, though the exact mechanism of catalysis is not known. It is thought
that this binding stabilizes the transition state through electrostatic effects, accounting for the
dramatic increase in the reaction rate in the presence of the mutase or upon addition of a
specifically-placed cation in the active site.
https://www.creative-enzymes.com/resource/isomerase-
introduction_23.html
19. ■ Intramolecular oxidoreduction
Isopentenyl-diphosphate delta isomerase type I (also known as IPP isomerase) is seen
in cholesterol synthesis and in particular it catalyzes the conversion of isopentenyl
diphosphate (IPP) to dimethylallyl diphosphate (DMAPP). IPP isomerase catalyzes this
reaction by the stereoselective antarafacial transposition of a single proton. The double
bond is protonated at C4 to form a tertiary carbocation intermediate at C3. The adjacent
carbon, C2, is deprotonated from the opposite face to yield a double bond. In effect, the double
bond is shifted over.
https://www.creative-enzymes.com/resource/isomerase-
introduction_23.html
C4
C3
C2
20. WHERE CAN YOU COME ACROSS THESE ENZYMES?
■ The role of isomerase in human disease:
Phosphohexose isomerase deficiency
The disease referred to as triosephosphate isomerase deficiency (TPI), is a severe autosomal
recessive inherited multisystem disorder of glycolytic metabolism. It is characterized by
hemolytic anemia and neurodegeneration, and is caused by anaerobic metabolic dysfunction.
This dysfunction results from a missense mutation that effects the encoded TPI protein.
TPI deficiency is very rare with less than 50 cases reported in literature.
Phosphohexose isomerase deficiency
Phosphohexose Isomerase Deficiency (PHI) is also known as phosphoglucose isomerase
deficiency or Glucose-6-phosphate isomerase deficiency, and is a hereditary enzyme
deficiency. This disease is centered on the glucose-6-phosphate protein. PHI is the result of
a dimeric enzyme that catalyzes the reversible interconversion of fructose-6-phosphate and
gluose-6-phosphate.
In humans deficiency of PHI leads to hemolytic syndrome, which is characterized by a
diminished erythrocyte number, lower hematocrit, lower hemoglobin, higher number of
reticulocytes and plasma bilirubin concentration, as well as increased liver- and spleen-
somatic indices, was exclusively manifested in homozygous mutants.
21. ■ Industrial applications
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.
The efficient isomerization of xylose to xylulose by glucose isomerase is found naturally in
bacteria that feed on decaying plant matter.
The isomerization of xylose to xylulose has its own commercial applications as interest
in biofuels has increased.
Its most common industrial use is in the production of ethanol, achieved by
the fermentation of xylulose.
• Merkle S, Pretsch W (1993). "Glucose-6-phosphate isomerase deficiency associated with nonspherocytic
hemolytic anemia in the mouse: an animal model for the human disease" (PDF). Blood. 81 (1): 206–
13. PMID 8417789.
• "Triose phosphate isomerase deficiency -TPI" (PDF). Retrieved 26 November 2013.
• Bhosale SH, Rao MB, Deshpande VV (Jun 1996). "Molecular and industrial aspects of glucose
isomerase". Microbiological Reviews. 60 (2): 280–300. PMC 239444. PMID 8801434