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Isomerases facilitate intramolecular rearrangements in which [[chemical bond|bonds]] are [[Bond cleavage|broken]] and formed. The general form of such a reaction is as follows: :<math chem>\ce{A-B} \quad \xrightarrow[\text{ isomerase }]{} \quad \ce{B-A}</math> There is only one [[Enzyme substrate (biology)|substrate]] yielding one product. This product has the same [[chemical formula|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== {{multiple image | align = right | direction = vertical | header = Examples of isomers | width = 200 | image1 = Hexane isomers.svg | alt1 = zig-zag models of hexane and four isomers | caption1 = The structural isomers of hexane | image2 = Cis-trans example.svg | alt2 = zig-zag model of cis-2-butene vs trans-2-butene | caption2 = Cis-2-butene and Trans-2-butene | image3 = Epimers-Glucose Mannose.png | alt3 = projection of D-glucose and D-mannose | caption3 = Epimers: D-glucose and D-mannose }} Isomerases [[catalysis|catalyze]] changes within one molecule.<ref>{{cite book|title=Enzyme nomenclature, 1978 recommendations of the Nomenclature Committee of the International Union of Biochemistry on the nomenclature and classification of enzymes.|url=https://archive.org/details/enzymenomenclatu0000inte|url-access=registration|year=1979|publisher=Academic Press|location=New York|isbn=9780323144605}}</ref> They convert one isomer to another, meaning that the end product has the same molecular formula but a different physical structure. [[Isomer]]s themselves exist in many varieties but can generally be classified as [[structural isomer]]s or [[stereoisomerism|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 ([[2-methylpentane]], [[3-methylpentane]], [[2,2-dimethylbutane]], and [[2,3-dimethylbutane]]). 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.<ref name=gold>{{cite book | last = McNaught | first = A. D. | name-list-style = vanc | title = Compendium of Chemical Terminology | edition = 2nd | year = 1997 | publisher = Blackwell Scientific Publications | location = Oxford | isbn = 978-0-9678550-9-7 | url = http://goldbook.iupac.org }}</ref> 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 [[activation energy|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.<ref name=organic>{{cite book | last1 = Whitesell | first1 = James K. | first2 = Marye Anne | last2 = Fox | name-list-style = vanc | title = Organic Chemistry | year = 2004 | publisher = Jones and Bartlett | location = Sudbury, Mass. | isbn = 978-0-7637-2197-8 | pages = 220–222 | edition = 3rd }}</ref> Calculating isomerase [[enzyme kinetics|kinetics]] from experimental data can be more difficult than for other enzymes because the use of [[Reaction progress kinetic analysis|product inhibition experiments]] is impractical.<ref name=kinetics>{{cite book |author-link1=Athel Cornish-Bowden| last = Cornish-Bowden | first = Athel | name-list-style = vanc | title = Fundamentals of Enzyme Kinetics | publisher=Wiley-VCH | location = Weinheim | isbn = 978-3-527-66548-8 | pages = 238–241 | edition = 4th | date = 2013-02-22 }}</ref> That is, isomerization is not an [[irreversible process|irreversible reaction]] since a reaction vessel will contain one substrate and one product so the typical simplified model for calculating [[Michaelis–Menten kinetics|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 [[Isotopic labeling|isotope exchange]] to measure indirectly the [[Reversible reaction|interconversion]] of the free enzyme between its two forms. The radiolabeled substrate and product [[diffusion|diffuse]] in a time-dependent manner. When the system reaches [[chemical equilibrium|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.<ref name=proline>{{cite journal | vauthors = Fisher LM, Albery WJ, Knowles JR | title = Energetics of proline racemase: tracer perturbation experiments using [14C]proline that measure the interconversion rate of the two forms of free enzyme | journal = Biochemistry | volume = 25 | issue = 9 | pages = 2538–42 | date = May 1986 | pmid = 3521737 | doi = 10.1021/bi00357a038 }}</ref> The earliest use of this technique elucidated the kinetics and [[Reaction mechanism|mechanism]] underlying the action of [[phosphoglucomutase]], favoring the model of indirect transfer of [[phosphate]] with one [[Reaction intermediate|intermediate]] and the direct transfer of [[glucose]].<ref>{{cite journal | vauthors = Britton HG, Clarke JB | title = The mechanism of the phosphoglucomutase reaction. Studies on rabbit muscle phosphoglucomutase with flux techniques | journal = The Biochemical Journal | volume = 110 | issue = 2 | pages = 161–80 | date = Nov 1968 | pmid = 5726186 | pmc = 1187194 | doi=10.1042/bj1100161}}</ref> 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-determining step|rate-limiting]] and that these enzyme forms may differ just in the [[protonation]] at the [[acid]]ic and [[Base (chemistry)|basic]] [[functional group|groups]] of the [[active site]].<ref name=proline /> ==Nomenclature== Generally, "the names of isomerases are formed as "''substrate'' isomerase" (for example, [[enoyl CoA isomerase]]), or as "''substrate'' ''type of isomerase''" (for example, [[phosphoglucomutase]])."<ref name=essential>{{cite book | last = Bruice | first = Paula Yurkanis | name-list-style = vanc | title = Essential Organic Chemistry | year = 2010 | publisher = Prentice Hall | location = Upper Saddle River, N.J. | isbn = 978-0-321-59695-6 | edition = 2nd }}</ref> ==Classification== Enzyme-catalyzed reactions each have a uniquely assigned classification number. Isomerase-catalyzed reactions have their own [[Enzyme Commission number|EC]] category: EC 5.<ref name=nomenclature /> Isomerases are further classified into six subclasses: ===Racemases, epimerases=== This category (EC 5.1) includes ([[racemase]]s) and [[epimerase]]s). These isomerases invert [[stereochemistry]] at the target [[stereocenter|chiral carbon]]. [[Epimerase and racemase|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 [[enantiomer]]ic 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 [[epimer]]s, which differ from one another in absolute configuration at just one chiral carbon.<ref name=gold /> 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: {| class="wikitable" |+ Racemases and epimerases: ! EC number || Description || Examples |- | align=''center'' | [[:Category:EC 5.1.1|EC 5.1.1]] || Acting on Amino Acids and Derivative || [[alanine racemase]], [[methionine racemase]] |- | align=''center'' | [[:Category:EC 5.1.2|EC 5.1.2]] || Acting on Hydroxy Acids and Derivatives || [[lactate racemase]], [[tartrate epimerase]] |- | align=''center'' | [[:Category:EC 5.1.3|EC 5.1.3]] || Acting on Carbohydrates and Derivatives || [[ribulose-phosphate 3-epimerase]], [[UDP-glucose 4-epimerase]] |- | align=''center'' | [[:Category:EC 5.1.99|EC 5.1.99]] || Acting on Other Compounds || [[methylmalonyl CoA epimerase]], [[hydantoin racemase]] |- |} ===Cis-trans isomerases=== This category (EC 5.2) includes enzymes that catalyze the isomerization of [[Cis–trans isomerism|cis-trans isomer]]s. [[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.<ref name=gold /> This category is not broken down any further. All entries presently include: [[File:Proline-cis-trans-isomerisation.svg|thumbnail|Conversion mediated by peptidylprolyl isomerase (PPIase).]] {| class="wikitable" |+ Cis-trans isomerases: ! EC number || Examples |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.1]] || [[Maleate isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.2]] || [[Maleylacetoacetate isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.4]] || [[Maleylpyruvate isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.5]] || [[Linoleate isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.6]] || [[Furylfuramide isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.8]] || [[Peptidylprolyl isomerase A|Peptidylprolyl isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.9]] || [[Farnesol 2-isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.10]] || [[2-chloro-4-carboxymethylenebut-2-en-1,4-olide isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.12]] || [[Zeta-carotene isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.13]] || [[Prolycopene isomerase]] |- | align=''center'' | [[:Category:EC 5.2.1|EC 5.2.1.14]] || [[Beta-carotene isomerase]] |- |} ===Intramolecular oxidoreductases=== This category (EC 5.3) includes [[Intramolecular reaction|intramolecular]] [[oxidoreductase]]s. These isomerases catalyze the transfer of [[electron]]s from one part of the molecule to another. In other words, they catalyze the [[Redox|oxidation]] of one part of the molecule and the concurrent reduction of another part.<ref name=nomenclature>{{cite book | last = Webb | first = Edwin C. | name-list-style = vanc | title = Enzyme nomenclature 1992 : recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes | year = 1992 | publisher = Published for the International Union of Biochemistry and Molecular Biology by Academic Press | location = San Diego | isbn = 978-0-12-227164-9 | edition = 6th | url-access = registration | url = https://archive.org/details/enzymenomenclatu0000inte_d6c2 }}</ref> Sub-categories of this class are: [[File:Phosphoribosylanthranilate isomerase.jpg|thumbnail|reaction catalyzed by phosphoribosylanthranilate isomerase]] {| class="wikitable" |+ Intramolecular oxidoreductases: ! EC number || Description || Examples |- | align=''center'' | [[:Category:EC 5.3.1|EC 5.3.1]] || Interconverting Aldoses and Ketoses || [[Triose-phosphate isomerase]], [[Ribose-5-phosphate isomerase]] |- | align=''center'' | [[:Category:EC 5.3.2|EC 5.3.2]] || Interconverting Keto- and Enol-Groups || [[Phenylpyruvate tautomerase]], [[Oxaloacetate tautomerase]] |- | align=''center'' | [[:Category:EC 5.3.3|EC 5.3.3]] || Transposing C=C Double Bonds || [[Steroid Delta-isomerase]], [[L-dopachrome isomerase]] |- | align=''center'' | [[:Category:EC 5.3.4|EC 5.3.4]] || Transposing S-S Bonds || [[Protein disulfide-isomerase]] |- | align=''center'' | [[:Category:EC 5.3.99|EC 5.3.99]] || Other Intramolecular Oxidoreductases || [[Prostaglandin-D synthase]], [[Allene-oxide cyclase]] |- |} ===Intramolecular transferases=== This category (EC 5.4) includes intramolecular [[transferase]]s ([[mutase]]s). These isomerases catalyze the transfer of [[functional group]]s from one part of a molecule to another.<ref name=nomenclature /> Phosphotransferases (EC 5.4.2) were categorized as transferases (EC 2.7.5) with regeneration of donors until 1983.<ref>{{cite book|title=The Enzyme List Class 5 - Isomerases|year=2010|publisher=Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB)|url=http://www.enzyme-database.org/downloads/ec5.pdf}}</ref> This sub-class can be broken down according to the functional group the enzyme transfers: [[File:PEP to PPR.png|thumbnail|reaction catalyzed by phosphoenolpyruvate mutase]] {| class="wikitable" |+ Intramolecular transferases: ! EC number || Description || Examples |- | align=''center'' | [[:Category:EC 5.4.1|EC 5.4.1]] || Transferring Acyl Groups || [[Lysolecithin acylmutase]], [[Precorrin-8X methylmutase]] |- | align=''center'' | [[:Category:EC 5.4.2|EC 5.4.2]] || Phosphotransferases (Phosphomutases) || [[Phosphoglucomutase]], [[Phosphopentomutase]] |- | align=''center'' | [[:Category:EC 5.4.3|EC 5.4.3]] || Transferring Amino Groups || [[Beta-lysine 5,6-aminomutase]], [[Tyrosine 2,3-aminomutase]] |- | align=''center'' | [[:Category:EC 5.4.4|EC 5.4.4]] || Transferring hydroxy groups || [[(hydroxyamino)benzene mutase]], [[Isochorismate synthase]] |- | align=''center'' | [[:Category:EC 5.4.99|EC 5.4.99]] || Transferring Other Groups || [[Methylaspartate mutase]], [[Chorismate mutase]] |- |} ===Intramolecular lyases=== This category (EC 5.5) includes intramolecular [[lyase]]s. 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 [[covalent bond|covalently]] attached to the molecule."<ref name=nomenclature /> Some of these catalyzed reactions involve the breaking of a ring structure. This category is not broken down any further. All entries presently include: [[File:Ent-CDP synthase reaction.png|thumbnail|reaction catalyzed by ent-Copalyl diphosphate synthase]] {| class="wikitable" |+ Intramolecular lyases: ! EC number || Examples |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.1]] || [[Muconate cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.2]] || [[3-carboxy-cis,cis-muconate cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.3]] || [[Tetrahydroxypteridine cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.4]] || [[Inositol-3-phosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.5]] || [[Carboxy-cis,cis-muconate cyclase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.6]] || [[Chalcone isomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.7]] || [[Chloromuconate cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.8]] || [[bornyl diphosphate synthase|(+)-bornyl diphosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.9]] || [[Cycloeucalenol cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.10]] || [[Alpha-pinene-oxide decyclase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.11]] || [[Dichloromuconate cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.12]] || [[Copalyl diphosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.13]] || [[Ent-copalyl diphosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.14]] || [[Syn-copalyl-diphosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.15]] || [[Terpentedienyl-diphosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.16]] || [[Halimadienyl-diphosphate synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.17]] || [[(S)-beta-macrocarpene synthase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.18]] || [[Lycopene epsilon-cyclase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.19]] || [[Lycopene beta-cyclase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.20]] || [[Prosolanapyrone-III cycloisomerase]] |- | align=''center'' | [[:Category:EC 5.5.1|EC 5.5.1.n1]] || D-ribose pyranase |- |} ==Mechanisms of isomerases== ===Ring expansion and contraction via tautomers=== [[File:Phosphoglucose Isomerase Mechanism.jpg|thumbnail|The isomerization of glucose-6-phosphate by glucose-6-phosphate isomerase]] A classic example of ring opening and contraction is the isomerization of [[glucose]] (an [[aldehyde]] with a six-membered ring) to [[fructose]] (a [[ketone]] with a five-membered ring). The conversion of D-glucose-6-phosphate to D-fructose-6-phosphate is catalyzed by [[glucose-6-phosphate isomerase]], an intramolecular [[oxidoreductase]]. The overall reaction involves the opening of the ring to form an aldose via [[acid catalysis|acid/base catalysis]] and the subsequent formation of a cis-endiol intermediate. A ketose is then formed and the ring is closed again. Glucose-6-phosphate first binds to the [[active site]] of the isomerase. The isomerase opens the ring: its [[histidine|His388]] residue [[protonation|protonates]] the oxygen on the glucose ring (and thereby breaking the O5-C1 bond) in conjunction with [[lysine|Lys518]] deprotonating the C1 [[hydroxyl]] oxygen. The ring opens to form a straight-chain [[aldose]] with an acidic C2 proton. The C3-C4 bond rotates and [[glutamic acid|Glu357]] (assisted by His388) depronates C2 to form a double bond between C1 and C2. A [[enol|cis-endiol]] intermediate is created and the C1 oxygen is protonated by the catalytic residue, accompanied by the deprotonation of the endiol C2 oxygen. The straight-chain [[ketose]] is formed. To close the fructose ring, the reverse of ring opening occurs and the ketose is protonated.<ref name=phosphoglucose>{{cite journal | vauthors = Solomons JT, Zimmerly EM, Burns S, Krishnamurthy N, Swan MK, Krings S, Muirhead H, Chirgwin J, Davies C | title = The crystal structure of mouse phosphoglucose isomerase at 1.6A resolution and its complex with glucose 6-phosphate reveals the catalytic mechanism of sugar ring opening | journal = Journal of Molecular Biology | volume = 342 | issue = 3 | pages = 847–60 | date = Sep 2004 | pmid = 15342241 | doi = 10.1016/j.jmb.2004.07.085 }}</ref> ===Epimerization=== [[File:Ribulose-phosphate 3-epimerase reaction.jpg|thumbnail|left|The conversion of ribulose-5-phosphate to xylulose-5-phosphate]] An example of epimerization is found in the Calvin cycle when D-ribulose-5-phosphate is converted into D-xylulose-5-phosphate by [[ribulose-phosphate 3-epimerase]]. The substrate and product differ only in [[stereochemistry]] at the third carbon in the chain. The underlying mechanism involves the deprotonation of that third carbon to form a reactive [[enol]]ate intermediate. The enzyme's active site contains two [[aspartate|Asp]] residues. After the substrate binds to the enzyme, the first Asp deprotonates the third carbon from one side of the molecule. This leaves a planar [[Orbital hybridisation|sp<sup>2</sup>-hybridized]] intermediate. The second Asp is located on the opposite side of the active side and it protonates the molecule, effectively adding a proton from the back side. These coupled steps invert stereochemistry at the third carbon.<ref>{{cite journal | vauthors = Terada T, Mukae H, Ohashi K, Hosomi S, Mizoguchi T, Uehara K | title = Characterization of an enzyme which catalyzes isomerization and epimerization of D-erythrose 4-phosphate | journal = European Journal of Biochemistry | volume = 148 | issue = 2 | pages = 345–51 | date = Apr 1985 | pmid = 3987693 | doi = 10.1111/j.1432-1033.1985.tb08845.x }}</ref> ===Intramolecular transfer=== [[File:Chorismate mutase mechanism.gif|thumbnail|A proposed mechanism for chorismate mutase. Clark, T., Stewart, J.D. and Ganem, B. Transition-state analogue inhibitors of chlorismate mutase. Tetrahedron 46 (1990) 731–748. © IUBMB 2001]] [[Chorismate mutase]] is an intramolecular transferase and it catalyzes the conversion of [[Chorismic acid|chorismate]] to [[Prephenic acid|prephenate]], used as a precursor for [[tyrosine|L-tyrosine]] and [[phenylalanine|L-phenylalanine]] in some plants and bacteria. This reaction is a [[Claisen rearrangement]] that can proceed with or without the isomerase, though the rate increases 10<sup>6</sup> fold in the presence of chorismate mutase. The reaction goes through a [[Cyclohexane conformation|chair]] [[transition state]] with the substrate in a trans-diaxial position.<ref>{{cite book | last = Bugg | first = TDH | name-list-style = vanc | chapter = Chapter 10: Isomerases | title = Introduction to Enzyme and Coenzyme Chemistry | edition = 3rd | year = 2012 | publisher = Wiley | isbn = 978-1-118-34896-3 }}</ref> 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.<ref>{{cite journal | vauthors = Kast P, Grisostomi C, Chen IA, Li S, Krengel U, Xue Y, Hilvert D | title = A strategically positioned cation is crucial for efficient catalysis by chorismate mutase | journal = The Journal of Biological Chemistry | volume = 275 | issue = 47 | pages = 36832–8 | date = Nov 2000 | pmid = 10960481 | doi = 10.1074/jbc.M006351200 | doi-access = free }}</ref> ===Intramolecular oxidoreduction=== [[File:IPP isomerase mechanism.png|thumbnail|left|Conversion by IPP isomerase]] [[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). In this isomerization reaction a stable carbon-carbon double bond is rearranged top create a highly [[electrophile|electrophilic]] [[allylic rearrangement|allylic isomer]]. IPP isomerase catalyzes this reaction by the [[stereoselectivity|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.<ref>{{cite journal | vauthors = Zheng W, Sun F, Bartlam M, Li X, Li R, Rao Z | title = The crystal structure of human isopentenyl diphosphate isomerase at 1.7 A resolution reveals its catalytic mechanism in isoprenoid biosynthesis | journal = Journal of Molecular Biology | volume = 366 | issue = 5 | pages = 1447–58 | date = Mar 2007 | pmid = 17250851 | doi = 10.1016/j.jmb.2006.12.055 }}</ref> In effect, the double bond is shifted over. ==The role of isomerase in human disease== Isomerase plays a role in human disease. Deficiencies of this enzyme can cause disorders in humans. ===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. PHI is the second most frequent [[erthoenzyopathy]] in [[glycolysis]] besides [[pyruvate kinase deficiency]], and is associated with non-spherocytic haemolytic anaemia of variable severity.<ref name=GDI>{{cite journal | vauthors = Kugler W, Lakomek M | title = Glucose-6-phosphate isomerase deficiency | journal = Baillière's Best Practice & Research. Clinical Haematology | volume = 13 | issue = 1 | pages = 89–101 | date = Mar 2000 | pmid = 10916680 | doi = 10.1053/beha.1999.0059 }}</ref><ref name="Hemolytic Anemia" /> This disease is centered on the glucose-6-phosphate protein. This protein can be found in the secretion of some cancer cells.<ref name="PHI Deficiency">{{cite journal | vauthors = Krone W, Schneider G, Schulz D, Arnold H, Blume KG | title = Detection of phosphohexose isomerase deficiency in human fibroblast cultures | journal = Humangenetik | volume = 10 | issue = 3 | pages = 224–30 | date = 1 January 1970 | pmid = 5475507 | doi = 10.1007/BF00295784 | s2cid = 34123426 }}</ref> PHI is the result of a dimeric enzyme that catalyses the reversible interconversion of fructose-6-phosphate and gluose-6-phosphate.<ref name="GDI"/> PHI is a very rare disease with only 50 cases reported in literature to date.<ref name=GDI /> Diagnosis is made on the basis of the clinical picture in association with biochemical studies revealing erythrocyte GPI deficiency (between 7 and 60% of normal) and identification of a mutation in the GPI gene by molecular analysis.<ref name=GDI /> The deficiency of phosphohexose isomerase can lead to a condition referred to as [[hemolytic syndrome]]. As in humans, the 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.<ref name="Hemolytic Anemia">{{cite journal | vauthors = Merkle S, Pretsch W | title = Glucose-6-phosphate isomerase deficiency associated with nonspherocytic hemolytic anemia in the mouse: an animal model for the human disease | journal = Blood | volume = 81 | issue = 1 | pages = 206–13 | year = 1993 | doi = 10.1182/blood.V81.1.206.206 | pmid = 8417789 | url = http://www.bloodjournal.org/content/bloodjournal/81/1/206.full.pdf | doi-access = free }}</ref> ===Triosephosphate isomerase deficiency=== The disease referred to as triosephosphate isomerase deficiency (TPI), is a severe autosomal recessive inherited multisystem disorder of [[glycolytic metabolism]].<ref name=Orphanet>{{cite web | last = Orosz | first = Pr Ferenc | name-list-style = vanc | title = Triose phosphate-isomerase deficiency|url=http://www.orpha.net/consor/cgi-bin/OC_Exp.php?lng=en&Expert=868|work=Orphanet|access-date=14 November 2013}}</ref> 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.<ref name="TPI Deficiency">{{cite journal | vauthors = Celotto AM, Frank AC, Seigle JL, Palladino MJ | title = Drosophila model of human inherited triosephosphate isomerase deficiency glycolytic enzymopathy | journal = Genetics | volume = 174 | issue = 3 | pages = 1237–46 | date = Nov 2006 | pmid = 16980388 | pmc = 1667072 | doi = 10.1534/genetics.106.063206 }}</ref> The most common mutation is the substitution of gene, Glu104Asp, which produces the most severe [[phenotype]], and is responsible for approximately 80% of clinical TPI deficiency.<ref name=Orphanet /> TPI deficiency is very rare with less than 50 cases reported in literature.<ref name="TPI paper" /> Being an autosomal recessive inherited disease, TPI deficiency has a 25% recurrence risk in the case of heterozygous parents.<ref name=Orphanet /><ref name="TPI paper">{{cite journal | vauthors = Oláh J, Orosz F, Keserü GM, Kovári Z, Kovács J, Hollán S, Ovádi J | title = Triosephosphate isomerase deficiency: a neurodegenerative misfolding disease | journal = Biochemical Society Transactions | volume = 30 | issue = 2 | pages = 30–8 | date = Apr 2002 | pmid = 12023819 | doi = 10.1042/bst0300030 | url = http://www.enzim.hu/data/pdf/12023819.pdf | access-date = 2013-11-27 | archive-url = https://web.archive.org/web/20131203012215/http://www.enzim.hu/data/pdf/12023819.pdf | archive-date = 2013-12-03 | url-status = dead }}</ref> It is a congenital disease that most often occurs with hemolytic anemia and manifests with jaundice.<ref name=Orphanet /> Most patients with TPI for Glu104Asp mutation or heterozygous for a TPI null allele and Glu104Asp have a life expectancy of infancy to early childhood. TPI patients with other mutations generally show longer life expectancy. There are only two cases of individuals with TPI living beyond the age of 6. These cases involve two brothers from Hungary, one who did not develop neurological symptoms until the age of 12, and the older brother who has no neurological symptoms and suffers from anemia only.<ref name="Anemia fact">{{cite journal | vauthors = Hollán S, Fujii H, Hirono A, Hirono K, Karro H, Miwa S, Harsányi V, Gyódi E, Inselt-Kovács M | title = Hereditary triosephosphate isomerase (TPI) deficiency: two severely affected brothers one with and one without neurological symptoms | journal = Human Genetics | volume = 92 | issue = 5 | pages = 486–90 | date = Nov 1993 | pmid = 8244340 | doi = 10.1007/bf00216456 | s2cid = 3110178 }}</ref> Individuals with TPI show obvious symptoms after 6–24 months of age. These symptoms include: dystonia, tremor, dyskinesia, pyramidal tract signs, cardiomyopathy and spinal motor neuron involvement.<ref name=Orphanet /> Patients also show frequent respiratory system bacterial infections.<ref name=Orphanet /> TPI is detected through deficiency of enzymatic activity and the build-up of dihyroxyacetone phosphate(DHAP), which is a toxic substrate, in erythrocytes.<ref name=Orphanet /><ref name="TPI paper" /> This can be detected through physical examination and a series of lab work. In detection, there is generally myopathic changes seen in muscles and chronic axonal neuropathy found in the nerves.<ref name=Orphanet /> Diagnosis of TPI can be confirmed through molecular genetics.<ref name=Orphanet /> Chorionic villus DNA analysis or analysis of fetal red cells can be used to detect TPI in antenatal diagnosis.<ref name=Orphanet /> '''Treatment''' for TPI is not specific, but varies according to different cases. Because of the range of symptoms TPI causes, a team of specialist may be needed to provide treatment to a single individual. That team of specialists would consists of pediatricians, cardiologists, neurologists, and other healthcare professionals, that can develop a comprehensive plan of action.<ref name="Treatment of TPI">{{cite web|title=Triosephosphate Isomerase Deficiency|url=http://www.rarediseases.org/rare-disease-information/rare-diseases/byID/1183/printFullReport|publisher=NORD|access-date=14 December 2013}}</ref> Supportive measures such as red cell transfusions in cases of severe anaemia can be taken to treat TPI as well. In some cases, spleen removal (splenectomy) may improve the anaemia. There is no treatment to prevent progressive neurological impairment of any other non-haematological clinical manifestation of the diseases.<ref name=enerca>{{cite web|title=Triose phosphate isomerase deficiency -TPI|url=http://www.enerca.org/media/upload/pdf/triose_phosphate_isomerase_deficiency-tpi_DOCUMENTS1_59.pdf|access-date=26 November 2013}}</ref> ==Industrial applications== By far the most common use of isomerases in industrial applications is in [[sugar]] manufacturing. Glucose isomerase (also known as [[xylose isomerase]]) catalyzes the conversion of D-[[xylose]] and D-[[glucose]] to D-[[xylulose]] and D-[[fructose]]. Like most sugar isomerases, glucose isomerase catalyzes the interconversion of [[aldose]]s and [[ketose]]s.<ref name=glucose>{{cite journal | vauthors = Bhosale SH, Rao MB, Deshpande VV | title = Molecular and industrial aspects of glucose isomerase | journal = Microbiological Reviews | volume = 60 | issue = 2 | pages = 280–300 | date = Jun 1996 | doi = 10.1128/mr.60.2.280-300.1996 | pmid = 8801434 | pmc=239444}}</ref> The conversion of glucose to fructose is a key component of [[high-fructose corn syrup]] production. [[Isomerization]] is more specific than older chemical methods of fructose production, resulting in a higher [[Yield (chemistry)|yield]] of fructose and no [[By-product|side products]].<ref name=glucose /> The fructose produced from this isomerization reaction is purer with no residual flavors from [[Contamination|contaminants]]. High-fructose corn syrup is preferred by many confectionery and soda manufacturers because of the high sweetening power of fructose (twice that of sucrose<ref>{{cite journal | last = Baker | first = S.A. | name-list-style = vanc | title = Pure fructose syrups | journal = Process Biochemistry | year = 1976 | volume = 11 | pages = 20–25 }}</ref>), its relatively low cost and its inability to crystallize. Fructose is also used as a sweetener for use by [[diabetics]].<ref name=glucose /> Major issues of the use of glucose isomerase involve its inactivation at higher temperatures and the requirement for a high [[pH]] (between 7.0 and 9.0) in the reaction environment. Moderately high temperatures, above 70&nbsp;°C, increase the yield of fructose by at least half in the isomerization step.<ref>{{cite journal | last1 = Antrim | first1 = RL| first2 = W | last2 = Colilla | first3 = BJ | last3 = Schnyder | name-list-style = vanc | title = Glucose isomerase production of high fructose syrups|journal=Applied Biochemistry and Bioengineering | year = 1979 | volume = 2 | pages = 97–155 }}</ref> The enzyme requires a [[divalent]] [[ion|cation]] such as [[cobalt|Co<sup>2+</sup>]] and [[magnesium|Mg<sup>2+</sup>]] for peak activity, an additional cost to manufacturers. Glucose isomerase also has a much higher affinity for xylose than for glucose, necessitating a carefully controlled environment.<ref name=glucose /> The isomerization of xylose to xylulose has its own commercial applications as interest in [[biofuel]]s has increased. This reaction is often seen naturally in [[Detritivore|bacteria]] that feed on decaying plant matter. Its most common industrial use is in the production of [[ethanol]], achieved by the [[fermentation]] of [[xylulose]]. The use of [[hemicellulose]] as source material is very common. Hemicellulose contains [[xylan]], which itself is composed of [[xylose]] in [[Glycosidic bond|β(1,4) linkages]].<ref>{{cite journal | vauthors = Wang PY, Shopsis C, Schneider H | title = Fermentation of a pentose by yeasts | journal = Biochemical and Biophysical Research Communications | volume = 94 | issue = 1 | pages = 248–54 | date = May 1980 | pmid = 6446306 | doi = 10.1016/s0006-291x(80)80213-0 }}</ref> The use of glucose isomerase very efficiently converts xylose to xylulose, which can then be acted upon by fermenting [[yeast]]. Overall, extensive research in genetic engineering has been invested into optimizing glucose isomerase and facilitating its recovery from industrial applications for re-use. Glucose isomerase is able to catalyze the isomerization of a range of other sugars, including D-[[ribose]], D-[[allose]] and L-[[arabinose]]. The most efficient substrates are those similar to glucose and xylose, having [[Cyclohexane conformation|equatorial]] [[hydroxyl]] groups at the third and fourth carbons.<ref>{{cite journal | last = Chen | first = WP | name-list-style = vanc | title = Glucose isomerase | journal = Process Biochemistry | date = August–September 1980 | volume = 15 | pages = 36–41 }}</ref> The current model for the mechanism of glucose isomerase is that of a [[Sigmatropic reaction|hydride shift]] based on [[X-ray crystallography]] and isotope exchange studies.<ref name=glucose /> ==Membrane-associated isomerases== Some isomerases associate with [[biological membranes]] as [[peripheral membrane protein]]s or anchored through a single [[transmembrane helix]],<ref>[http://membranome.org/protein_classes/13 Superfamilies of single-pass transmembrane lyases] in [[Membranome database]]</ref> for example isomerases with the [[thioredoxin domain]], and certain [[prolyl isomerase]]s. == References == 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