enzymology Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

, a xylose isomerase () is an

enzyme Enzymes () are proteins that act as biological catalysts by accelerating chemical reactions. The molecules upon which enzymes may act are called substrates, and the enzyme converts the substrates into different molecules known as products. A ...

that catalyzes the interconversion of

D-xylose Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a monosaccharide of the aldopentose type, which means that it contains five carbon atoms and includes an aldehyde functional gro ...

and D-xylulose. This enzyme belongs to the family of

isomerase 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: A–B � ...

s, specifically those intramolecular

oxidoreductase In biochemistry, an oxidoreductase is an enzyme that catalyzes the transfer of electrons from one molecule, the reductant, also called the electron donor, to another, the oxidant, also called the electron acceptor. This group of enzymes usually ut ...

s interconverting

aldose An aldose is a monosaccharide (a simple sugar) with a carbon backbone chain with a carbonyl group on the endmost carbon atom, making it an aldehyde, and hydroxyl groups connected to all the other carbon atoms. Aldoses can be distinguished from keto ...

s and

ketose A ketose is a monosaccharide containing one ketone group per molecule. The simplest ketose is dihydroxyacetone, which has only three carbon atoms. It is the only ketose with no optical activity. All monosaccharide ketoses are reducing sugars, be ...

s. The isomerase has now been observed in nearly a hundred species of bacteria.

Xylose Xylose ( grc, ξύλον, , "wood") is a sugar first isolated from wood, and named for it. Xylose is classified as a monosaccharide of the aldopentose type, which means that it contains five carbon atoms and includes an aldehyde functional gro ...

-isomerases are also commonly called fructose-isomerases due to their ability to interconvert glucose and fructose. The

systematic name A systematic name is a name given in a systematic way to one unique group, organism, object or chemical substance, out of a specific population or collection. Systematic names are usually part of a nomenclature. A semisystematic name or semitrivial ...

of this enzyme class is D-xylose aldose-ketose-isomerase. Other names in common use include D-xylose isomerase, D-xylose ketoisomerase, and D-xylose ketol-isomerase.

History

The activity of

was first observed by Mitsuhashi and Lampen in 1953 in the bacterium ''Lactobacillus pentosus''. Artificial production through transformed ''E.coli'' have also been successful. In 1957, the D-xylose isomerase activity on D-glucose conversion to D-fructose was noted by Kooi and Marshall. It is now known that isomerases have broad substrate specificity. Most pentoses and some hexoses are all substrates for D-xylose isomerase. Some examples include: D-ribose, L-arabinose, L-rhamnose, and D-allose. Conversion of glucose to fructose by xylose isomerase was first patented in the 1960s, however, the process was not industrially viable as the enzymes were suspended in solution, and recycling the enzyme was problematic. An immobile xylose isomerase that was fixed on a solid surface was first developed in Japan by Takanashi. These developments were essential to the development of

industrial fermentation Industrial fermentation is the intentional use of fermentation in manufacturing products useful to humans. In addition to the mass production of fermented foods and drinks, industrial fermentation has widespread applications in chemical industry ...

processes used in manufacturing

high fructose corn syrup High-fructose corn syrup (HFCS), also known as glucose–fructose, isoglucose and glucose–fructose syrup, is a sweetener made from corn starch. As in the production of conventional corn syrup, the starch is broken down into glucose by enzym ...

. The tertiary structure was determined for several xylose isomerases from microbes starting in the mid 1980s (''Streptomyces olivochromogenes'' in 1988, ''Streptomyces violaceoniger'' in 1988, ''Streptomyces rubiginosus'' in 1984, ''Arthrobacter B3728'' in 1986, ''Actinoplanes missouriensis'' in 1992, and ''Clostridium thermosulfurogenes'' in 1990).

Function

This enzyme participates in

pentose and glucuronate interconversions In chemistry, a pentose is a monosaccharide (simple sugar) with five carbon atoms. The chemical formula of many pentoses is , and their molecular weight is 150.13 g/mol.fructose Fructose, or fruit sugar, is a Ketose, ketonic monosaccharide, simple sugar found in many plants, where it is often bonded to glucose to form the disaccharide sucrose. It is one of the three dietary monosaccharides, along with glucose and galacto ...

and

mannose Mannose is a sugar monomer of the aldohexose series of carbohydrates. It is a C-2 epimer of glucose. Mannose is important in human metabolism, especially in the glycosylation of certain proteins. Several congenital disorders of glycosylation ...

metabolism. The most bio-available sugars according to the International Society of Rare Sugars are: glucose, galactose, mannose, fructose, xylose, ribose, and L-arabinose. Twenty hexoses and nine pentoses, including xylulose, were considered to be "rare sugars". Hence D-xylose isomerase is used to produce these rare sugars which have very important applications in biology despite their low abundance.

Characterization

Xylose isomerase that can be isolated from red Chinese rice wine, which contains the bacterium ''Lactobacillus xylosus''. This bacterium was mistakenly classified as a ''L. plantarum'', which normally grows on the sugar

L-arabinose Arabinose is an aldopentose – a monosaccharide containing five carbon atoms, and including an aldehyde (CHO) functional group. For biosynthetic reasons, most saccharides are almost always more abundant in nature as the "D"-form, or structural ...

, and rarely grown on D-xylose. ''L. xylosus'' was recognized to be distinct for its ability to grow on D-xylose. Xylose isomerase in ''L. xylosus'' has a molecular weight of about 183000 Daltons. Its optimum growth pH is about 7.5 for the ''L. lactis'', however strains such as the ''L.brevis'' xylose enzyme prefer a more alkaline environment. The ''L. lactis'' strain is stable over the pH range of 6.5 to 11.0, and the ''L. brevis'' enzyme, which is less tolerant of pH changes, show activity over the pH range of 5.7–7.0. Thermal tests were also done by Kei Y. and Noritaka T. and the xylose isomerase was found to be thermally stable to about 60 degrees Celsius

Active site and mechanism

Xylose isomerase has a structure that is based on eight alpha/beta barrels that create an active site holding two divalent magnesium ions. Xylose isomerase enzymes exhibit a

TIM barrel The TIM barrel (triose-phosphate isomerase), also known as an alpha/beta barrel, is a conserved protein fold consisting of eight alpha helices (α-helices) and eight parallel beta strands (β-strands) that alternate along the peptide backbone. ...

fold with the active site in the centre of the barrel and a

tetrameric A tetramer () (''tetra-'', "four" + ''-mer'', "parts") is an oligomer formed from four monomers or subunits. The associated property is called ''tetramery''. An example from inorganic chemistry is titanium methoxide with the empirical formula T ...

quaternary structure Protein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also refe ...

.Deprecated services < EMBL-EBI
/ref> PDB structures are available in the links in the infobox to the right. The protein is a

tetramer A tetramer () (''tetra-'', "four" + '' -mer'', "parts") is an oligomer formed from four monomers or subunits. The associated property is called ''tetramery''. An example from inorganic chemistry is titanium methoxide with the empirical formula Ti ...

where paired barrels are nearly coaxial, which form two cavities in which the divalent metals are both bound to one of the two cavities. The metals are in an octahedral geometry. Metal site 1 binds the substrate tightly, while metal site two binds the substrate loosely. Both share an acid residue Glutamic acid 216 of the enzyme that bridges the two cations. Two basic amino acids surround the negative charged

ligands In coordination chemistry, a ligand is an ion or molecule (functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's electro ...

to neutralize them. The second cavity faces the metal cavity and both cavities share the same access route. The second cavity is hydrophobic in nature, and has an important histidine residue that is activated by an

aspartate Aspartic acid (symbol Asp or D; the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. Like all other amino acids, it contains an amino group and a carboxylic acid. Its α-amino group is in the pro ...

residue that is

hydrogen bond In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a ...

ed to it. This histidine residue is important in the

isomerization In chemistry, isomerization or isomerisation is the process in which a molecule, polyatomic ion or molecular fragment is transformed into an isomer with a different chemical structure. Enolization is an example of isomerization, as is tautomeriz ...

of glucose. In the isomerization of glucose, Histidine 53 is used to catalyze the proton transfer of O1 to O5; the diagram for the ring opening mechanism is shown below. The first metal, mentioned earlier,

coordinates In geometry, a coordinate system is a system that uses one or more numbers, or coordinates, to uniquely determine the position of the points or other geometric elements on a manifold such as Euclidean space. The order of the coordinates is sig ...

to O3 and O4, and is used to dock the substrate. Structure and mechanism of xylose on glucose 2

In the isomerization of xylose, crystal data has shown that xylose sugar binds to the enzyme in an open chain conformation. Metal 1 binds to O2 and O4, and once bound, metal 2 binds to O1 and O2 in the transition state, and these interactions along with a lysine residue help catalyze the

hydride shift A sigmatropic reaction in organic chemistry is a pericyclic reaction wherein the net result is one σ-bond is changed to another σ-bond in an uncatalyzed intramolecular reaction. The name ''sigmatropic'' is the result of a compounding of the lon ...

necessary for isomerization. The transition state consists of a high energy

carbonium ion In chemistry, a carbonium ion is any cation that has a pentavalent carbon atom. The name carbonium may also be used for the simplest member of the class, properly called methanium (), where the five valences are filled with hydrogen atoms. The ...

that is stabilized through all the metal interactions with the sugar substrate. Structure and mechanism of xylose isomerization 2

Application in industry

The most widely used application of this enzyme is in the conversion of glucose to fructose to produce

(HFCS). There are three general steps in producing HFCS from starch: * enzymatic degradation of the starch using α-

amylase An amylase () is an enzyme that catalyses the hydrolysis of starch (Latin ') into sugars. Amylase is present in the saliva of humans and some other mammals, where it begins the chemical process of digestion. Foods that contain large amounts of ...

. Also known as liquification. * further degradation using

glucoamylase Glucan 1,4-α-glucosidase (EC 3.2.1.3, glucoamylase, amyloglucosidase', γ-amylase, lysosomal α-glucosidase, acid maltase, exo-1,4-α-glucosidase, glucose amylase, γ-1,4-glucan glucohydrolase, acid maltase, 1,4-α-D-glucan glucohydrolase) is an ...

and a debranching enzyme. * Production of fructose through xylose isomerase The process is carried out in

bioreactor A bioreactor refers to any manufactured device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical reaction, chemical process is carried out which involves organisms or biochemistry, ...

s at 60–65 °C. Enzymes become inactivated at high temperatures like this, and one focus of research has been engineering more thermostable versions of xylose isomerase and the other enzymes in the process. The enzymes are generally immobilized to increase throughput; better ways to do this has been another research focus. Xylose isomerase is one of the enzymes used by bacteria in nature to use

cellulose Cellulose is an organic compound with the formula , a polysaccharide consisting of a linear chain of several hundred to many thousands of β(1→4) linked D-glucose units. Cellulose is an important structural component of the primary cell wall ...

as food and another focus on industrial and academic research, has been developing versions of xylose isomerase that could be useful in the production of

biofuel Biofuel is a fuel that is produced over a short time span from biomass, rather than by the very slow natural processes involved in the formation of fossil fuels, such as oil. According to the United States Energy Information Administration (E ...

As a dietary supplement

Products containing Xylose-Isomerase are sold as

over-the-counter Over-the-counter (OTC) drugs are medicines sold directly to a consumer without a requirement for a prescription from a healthcare professional, as opposed to prescription drugs, which may be supplied only to consumers possessing a valid prescr ...

dietary supplements A dietary supplement is a manufactured product intended to supplement one's diet by taking a pill (pharmacy), pill, capsule (pharmacy), capsule, tablet (pharmacy), tablet, powder, or liquid. A supplement can provide nutrients either extr ...

to combat

fructose malabsorption Fructose, or fruit sugar, is a ketonic simple sugar found in many plants, where it is often bonded to glucose to form the disaccharide sucrose. It is one of the three dietary monosaccharides, along with glucose and galactose, that are absorbed ...

, primarily in Europe and under brand names including ''Fructaid'', ''Fructease'' and ''Fructosin''. Apart from general concerns over the effectiveness of OTC-enzymes, there is currently very limited research available on Xylose-Isomerase as a dietary supplement, with the sole scientific study indicating a positive effect on malabsorption-related nausea and abdominal pain, but none on bloating.