Xylose isomerase

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xylose isomerase
2glk.png
D-Xylose isomerase tetramer from Streptomyces rubiginosus PDB 2glk . [1] One monomer is coloured by secondary structure to highlight the TIM barrel architecture.
Identifiers
EC no. 5.3.1.5
CAS no. 9023-82-9
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In enzymology, a xylose isomerase (EC 5.3.1.5) is an enzyme that catalyzes the interconversion of D-xylose and D-xylulose. This enzyme belongs to the family of isomerases, specifically those intramolecular oxidoreductases interconverting aldoses and ketoses. The isomerase has now been observed in nearly a hundred species of bacteria. Xylose-isomerases are also commonly called fructose-isomerases due to their ability to interconvert glucose and fructose. The systematic name 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. [2]

Contents

History

The activity of D-xylose isomerase was first observed by Mitsuhashi and Lampen in 1953 in the bacterium Lactobacillus pentosus. [3] Artificial production through transformed E.coli have also been successful. [4] In 1957, the D-xylose isomerase activity on D-glucose conversion to D-fructose was noted by Kooi and Marshall. [5] 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. [6]

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. [6] An immobile xylose isomerase that was fixed on a solid surface was first developed in Japan by Takanashi. [6] These developments were essential to the development of industrial fermentation processes used in manufacturing high-fructose corn syrup. [7] : 27  [8] : 808–813  [9]

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). [7] : 366 

Function

This enzyme participates in pentose and glucuronate interconversions and fructose and mannose 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. [10]

Characterization

Xylose isomerase can be isolated from red Chinese rice wine, which contains the bacterium Lactobacillus xylosus. [11] This bacterium was mistakenly classified as a L. plantarum, which normally grows on the sugar L-arabinose, and rarely grown on D-xylose. L. xylosus was recognized to be distinct for its ability to grow on D-xylose. [12] Xylose isomerase in L. xylosus has a molecular weight of about 183000 daltons. [13] 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. [13] 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 [13]

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 fold with the active site in the centre of the barrel and a tetrameric quaternary structure. [14] PDB structures are available in the links in the infobox to the right. The protein is a tetramer 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 2 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 negatively charged ligands to neutralize them. The second cavity faces the metal cavity and both cavities share the same access route. The second cavity is hydrophobic, and has a histidine residue activated by an aspartate residue that is hydrogen bonded to it. This histidine residue is important in the isomerization of glucose. [15]

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 to O3 and O4, and is used to dock the substrate. [15]

ring opening mechanism of glucose Structure and mechanism of xylose on glucose 2.0.png
ring opening mechanism of glucose

In the isomerization of xylose, crystal data shows that xylose binds to the enzyme as an open chain. Metal 1 binds to O2 and O4, and once bound, metal 2 binds to O1 and O2 in the transition state. These interactions along with a lysine residue help catalyze the hydride shift necessary for isomerization. [16] [15] The transition state consists of a high energy carbonium ion that is stabilized through all the metal interactions with the sugar substrate. [15]

mechanism of xylose isomerization Structure and mechanism of xylose isomerization 2.0.png
mechanism of xylose isomerization

Application in industry

The most widely used application of this enzyme is in the conversion of glucose to fructose to produce high fructose corn syrup (HFCS). [7] : 27  There are three general steps in producing HFCS from starch: [8] : 808–813 

The process is carried out in bioreactors at 60–65 °C. [7] : 27  Enzymes become denatured at these temperatures, and one focus of research has been engineering more thermostable versions of xylose isomerase and the other enzymes in the process. [7] : 27  [17] The enzymes are generally immobilized to increase throughput, and finding better ways to do this has been another research focus. [7] : 358–360  [18]

Xylose isomerase is one of the enzymes used by bacteria in nature in order to utilize hemicellulose as an energy source, and another focus of industrial and academic research has been developing versions of xylose isomerase that could be useful in the production of biofuel. [7] : 358  [19] [20]

As a dietary supplement

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The conversion of glucose to fructose by xylose isomerase. Image taken from doi : 10.1017/S0007114521001215 under the conditions of CC BY 4.0 license; authors: Miles Benardout, Adam Le Gresley, Amr ElShaer and Stephen P. Wren.

The ability of xylose isomerase to convert between glucose and fructose has led to its proposal as a treatment for fructose malabsorption. [21] [22] This enzyme is used in industrial settings and has been shown to produce no allergic response in humans. [21]

Products containing xylose isomerase are sold as over-the-counter (OTC) dietary supplements to combat fructose malabsorption, under brand names including Fructaid, Fructease, Fructase, Fructose Digest and Fructosin. Apart from general concerns over the effectiveness of OTC-enzymes, [23] there is currently very limited research available on Xylose-Isomerase as a dietary supplement, [24] [21] with the sole scientific study [25] indicating a positive effect on malabsorption-related nausea and abdominal pain, but none on bloating. [22] [24] [21] This decrease in breath hydrogen excretion demonstrated in this study is a potential sign that fructose was absorbed much better. [21] However, the results of this study was not confirmed by other studies, and this study did not assess the long-term health effects and did not try to determine which patients are best suited to treatment with xylose isomerase, if at all. [21] [22]

Related Research Articles

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:

In organic chemistry, a tetrose is a monosaccharide with 4 carbon atoms. They have either an aldehyde functional group in position 1 (aldotetroses) or a ketone group in position 2 (ketotetroses).

<span class="mw-page-title-main">Fructose malabsorption</span> Medical condition

Fructose malabsorption, formerly named dietary fructose intolerance (DFI), is a digestive disorder in which absorption of fructose is impaired by deficient fructose carriers in the small intestine's enterocytes. This results in an increased concentration of fructose. Intolerance to fructose was first identified and reported in 1956.

<span class="mw-page-title-main">Glucose-6-phosphate isomerase</span> Mammalian protein found in Homo sapiens

Glucose-6-phosphate isomerase (GPI), alternatively known as phosphoglucose isomerase/phosphoglucoisomerase (PGI) or phosphohexose isomerase (PHI), is an enzyme that in humans is encoded by the GPI gene on chromosome 19. This gene encodes a member of the glucose phosphate isomerase protein family. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. In the cytoplasm, the gene product functions as a glycolytic enzyme that interconverts glucose-6-phosphate (G6P) and fructose-6-phosphate (F6P). Extracellularly, the encoded protein functions as a neurotrophic factor that promotes survival of skeletal motor neurons and sensory neurons, and as a lymphokine that induces immunoglobulin secretion. The encoded protein is also referred to as autocrine motility factor (AMF) based on an additional function as a tumor-secreted cytokine and angiogenic factor. Defects in this gene are the cause of nonspherocytic hemolytic anemia, and a severe enzyme deficiency can be associated with hydrops fetalis, immediate neonatal death and neurological impairment. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

<span class="mw-page-title-main">Transketolase</span> Enzyme involved in metabolic pathways

Transketolase is an enzyme that, in humans, is encoded by the TKT gene. It participates in both the pentose phosphate pathway in all organisms and the Calvin cycle of photosynthesis. Transketolase catalyzes two important reactions, which operate in opposite directions in these two pathways. In the first reaction of the non-oxidative pentose phosphate pathway, the cofactor thiamine diphosphate accepts a 2-carbon fragment from a 5-carbon ketose (D-xylulose-5-P), then transfers this fragment to a 5-carbon aldose (D-ribose-5-P) to form a 7-carbon ketose (sedoheptulose-7-P). The abstraction of two carbons from D-xylulose-5-P yields the 3-carbon aldose glyceraldehyde-3-P. In the Calvin cycle, transketolase catalyzes the reverse reaction, the conversion of sedoheptulose-7-P and glyceraldehyde-3-P to pentoses, the aldose D-ribose-5-P and the ketose D-xylulose-5-P.

Rhamnose is a naturally occurring deoxy sugar. It can be classified as either a methyl-pentose or a 6-deoxy-hexose. Rhamnose predominantly occurs in nature in its L-form as L-rhamnose (6-deoxy-L-mannose). This is unusual, since most of the naturally occurring sugars are in D-form. Exceptions are the methyl pentoses L-fucose and L-rhamnose and the pentose L-arabinose. However, examples of naturally-occurring D-rhamnose include some species of bacteria, such as Pseudomonas aeruginosa and Helicobacter pylori.

The Kiliani–Fischer synthesis, named for German chemists Heinrich Kiliani and Emil Fischer, is a method for synthesizing monosaccharides. It proceeds via synthesis and hydrolysis of a cyanohydrin, followed by reduction of the intermediate acid to the aldehyde, thus elongating the carbon chain of an aldose by one carbon atom while preserving stereochemistry on all the previously present chiral carbons. The new chiral carbon is produced with both stereochemistries, so the product of a Kiliani–Fischer synthesis is a mixture of two diastereomeric sugars, called epimers. For example, D-arabinose is converted to a mixture of D-glucose and D-mannose.

The L-arabinose operon, also called the ara or araBAD operon, is an operon required for the breakdown of the five-carbon sugar L-arabinose in Escherichia coli. The L-arabinose operon contains three structural genes: araB, araA, araD, which encode for three metabolic enzymes that are required for the metabolism of L-arabinose. AraB (ribulokinase), AraA, and AraD produced by these genes catalyse conversion of L-arabinose to an intermediate of the pentose phosphate pathway, D-xylulose-5-phosphate.

<span class="mw-page-title-main">Ribose 5-phosphate</span> Chemical compound

Ribose 5-phosphate (R5P) is both a product and an intermediate of the pentose phosphate pathway. The last step of the oxidative reactions in the pentose phosphate pathway is the production of ribulose 5-phosphate. Depending on the body's state, ribulose 5-phosphate can reversibly isomerize to ribose 5-phosphate. Ribulose 5-phosphate can alternatively undergo a series of isomerizations as well as transaldolations and transketolations that result in the production of other pentose phosphates as well as fructose 6-phosphate and glyceraldehyde 3-phosphate.

<span class="mw-page-title-main">Phosphopentose epimerase</span>

Phosphopentose epimerase encoded by the RPE gene is a metalloprotein that catalyzes the interconversion between D-ribulose 5-phosphate and D-xylulose 5-phosphate.

<span class="mw-page-title-main">6-phosphogluconolactonase</span> Cytosolic enzyme

6-Phosphogluconolactonase (EC 3.1.1.31, 6PGL, PGLS, systematic name 6-phospho-D-glucono-1,5-lactone lactonohydrolase) is a cytosolic enzyme found in all organisms that catalyzes the hydrolysis of 6-phosphogluconolactone to 6-phosphogluconic acid in the oxidative phase of the pentose phosphate pathway:

<span class="mw-page-title-main">Sucrose phosphorylase</span> Class of enzymes

Sucrose phosphorylase is an important enzyme in the metabolism of sucrose and regulation of other metabolic intermediates. Sucrose phosphorylase is in the class of hexosyltransferases. More specifically it has been placed in the retaining glycoside hydrolases family although it catalyzes a transglycosidation rather than hydrolysis. Sucrose phosphorylase catalyzes the conversion of sucrose to D-fructose and α-D-glucose-1-phosphate. It has been shown in multiple experiments that the enzyme catalyzes this conversion by a double displacement mechanism.

<span class="mw-page-title-main">Mannose phosphate isomerase</span>

Mannose-6 phosphate isomerase (MPI), alternately phosphomannose isomerase (PMI) is an enzyme which facilitates the interconversion of fructose 6-phosphate (F6P) and mannose-6-phosphate (M6P). Mannose-6-phosphate isomerase may also enable the synthesis of GDP-mannose in eukaryotic organisms. M6P can be converted to F6P by mannose-6-phosphate isomerase and subsequently utilized in several metabolic pathways including glycolysis and capsular polysaccharide biosynthesis. PMI is monomeric and metallodependent on zinc as a cofactor ligand. PMI is inhibited by erythrose 4-phosphate, mannitol 1-phosphate, and to a lesser extent, the alpha anomer of M6P.

<span class="mw-page-title-main">Xylose metabolism</span>

D-Xylose is a five-carbon aldose that can be catabolized or metabolized into useful products by a variety of organisms.

<span class="mw-page-title-main">D-xylulose reductase</span>

In enzymology, a D-xylulose reductase (EC 1.1.1.9) is an enzyme that is classified as an Oxidoreductase (EC 1) specifically acting on the CH-OH group of donors (EC 1.1.1) that uses NAD+ or NADP+ as an acceptor (EC 1.1.1.9). This enzyme participates in pentose and glucuronate interconversions; a set of metabolic pathways that involve converting pentose sugars and glucuronate into other compounds.

<span class="mw-page-title-main">L-arabinose isomerase</span>

In enzymology, a L-arabinose isomerase is an enzyme that catalyzes the chemical reaction

<span class="mw-page-title-main">L-ribulose-5-phosphate 4-epimerase</span>

In enzymology, a L-ribulose-5-phosphate 4-epimerase is an enzyme that catalyzes the interconversion of ribulose 5-phosphate and xylulose 5-phosphate in the oxidative phase of the Pentose phosphate pathway.

<span class="mw-page-title-main">Ribose-5-phosphate isomerase</span>

Ribose-5-phosphate isomerase (Rpi) encoded by the RPIA gene is an enzyme that catalyzes the conversion between ribose-5-phosphate (R5P) and ribulose-5-phosphate (Ru5P). It is a member of a larger class of isomerases which catalyze the interconversion of chemical isomers. It plays a vital role in biochemical metabolism in both the pentose phosphate pathway and the Calvin cycle. The systematic name of this enzyme class is D-ribose-5-phosphate aldose-ketose-isomerase.

The enzyme phosphoketolase(EC 4.1.2.9) catalyzes the chemical reactions

<span class="mw-page-title-main">Xylulokinase</span>

In enzymology, a xylulokinase is an enzyme that catalyzes the chemical reaction

References

  1. ↑ Katz AK, Li X, Carrell HL, Hanson BL, Langan P, Coates L, Schoenborn BP, Glusker JP, Bunick GJ (2006). "Locating active-site hydrogen atoms in D-xylose isomerase: Time-of-flight neutron diffraction". Proceedings of the National Academy of Sciences. 103 (22): 8342–8347. Bibcode:2006PNAS..103.8342K. doi: 10.1073/pnas.0602598103 . PMC   1482496 . PMID   16707576.
  2. ↑ Mu W, Hassanin HA, Zhou L, Jiang B (2018). "Chemistry Behind Rare Sugars and Bioprocessing". Journal of Agricultural and Food Chemistry. 66 (51): 13343–13345. doi:10.1021/acs.jafc.8b06293. PMID   30543101. S2CID   56145019.
  3. ↑ Mitsuhashi S, Lampen J (1953). "Conversion of D-xylose to D-xylulose in extracts of Lactobacillus pentosus" (PDF). Journal of Biological Chemistry. 204 (2): 1011–8. doi: 10.1016/S0021-9258(18)66103-4 . PMID   13117877. Archived (PDF) from the original on 2020-01-02. Retrieved 2017-01-16.
  4. ↑ Schomburg D (2001). Handbook of Enzymes. New York: Springer. pp. 259–260. ISBN   978-3-540-41008-9. Archived from the original on 2020-07-26. Retrieved 2020-07-19.
  5. ↑ Marshall R, Kooi E (1957). "Enzymic conversion of D-glucose to D-fructose". Science. 125 (3249): 648–9. Bibcode:1957Sci...125..648M. doi:10.1126/science.125.3249.648. PMID   13421660.
  6. 1 2 3 Jokela J, Pastinen O (2002). "Isomerization of pentose and hexose sugars by an enzyme reactor packed with cross-linked xylose isomerase crytals". Enzyme and Microbial Technology. 31 (1–2): 67–76. doi:10.1016/s0141-0229(02)00074-1.
  7. 1 2 3 4 5 6 7 Wong DW (1995). Food Enzymes Structure and Mechanism. Boston, MA: Springer US. ISBN   978-1-4757-2349-6.
  8. 1 2 Hobbs L (2009). "21 - Sweeteners from Starch: Production, Properties and Uses". In BeMiller JN, Whistler RL (eds.). Starch: chemistry and technology (3rd ed.). London: Academic Press/Elsevier. pp.  797–832. ISBN   978-0-12-746275-2.
  9. ↑ "Corn syrup and its culinary uses: Is it safe to consume?". The Times of India. ISSN   0971-8257. Archived from the original on 2024-02-16. Retrieved 2024-02-16.
  10. ↑ Beerens K (2012). "Enzymes for the biocatalytic production of rare sugars". J. Ind. Microbiol. Biotechnol. 39 (6): 823–834. doi: 10.1007/s10295-012-1089-x . PMID   22350065. S2CID   14877957.
  11. ↑ Kitahara K (1966). "Studies on Lactic Acid Bacteria". Nyusankin No Kenkyu: 67~69.
  12. ↑ Buchanan R, Gibbons N (1974). Bergey's Manual of Determining Bacteriology (8 ed.). Baltimore: The Williams and Wilkins Co. p. 584.
  13. 1 2 3 Yamanaka K, Takahara N (1977). "Purification and Properties of D-Xylose Isomerase from Lactobacillus xylosus". Agric. Biol. Chem. 41 (10): 1909–1915. doi: 10.1271/bbb1961.41.1909 .
  14. ↑ "Deprecated services < EMBL-EBI". Archived from the original on 2024-04-01. Retrieved 2015-02-06.
  15. 1 2 3 4 Blow D, Collyer C, Goldberg J, Smart O (1992). "Structure and Mechanism of D-xylose Isomerase". Faraday Discussions. 93 (93): 67–73. Bibcode:1992FaDi...93...67B. doi:10.1039/fd9929300067. PMID   1290940.
  16. ↑ Nam KH (2022). "Glucose Isomerase: Functions, Structures, and Applications". Applied Sciences. 12: 428. doi: 10.3390/app12010428 . Creative Commons by small.svg  This article incorporates textfrom this source, which is available under the CC BY 4.0 license.
  17. ↑ Qiu Y, Wu M, Bao H, Liu W, Shen Y (2023-09-01). "Engineering of Saccharomyces cerevisiae for co-fermentation of glucose and xylose: Current state and perspectives". Engineering Microbiology. 3 (3): 100084. doi: 10.1016/j.engmic.2023.100084 . ISSN   2667-3703.
  18. ↑ Volkin D, Klibanow A (1988). "Mechanism of thermoinacctivation of immobilized glucose isomerase". Biotechnol Bioeng. 33 (9): 1104–1111. doi:10.1002/bit.260330905. PMID   18588027. S2CID   39076432.
  19. ↑ Maris V, Antonius, et al. (2007). "Development of Efficient Xylose Fermentation in Saccharomyces Cerevisiae: Xylose Isomerase as a key component". Adv. Biochem. Eng. Biotechnol. Advances in Biochemical Engineering/Biotechnology. 108: 179–204. doi:10.1007/10_2007_057. ISBN   978-3-540-73650-9. PMID   17846724. Archived from the original on 2023-12-31. Retrieved 2023-12-31.
  20. ↑ Silva PC, Ceja-Navarro JA, Azevedo F, Karaoz U, Brodie EL, Johansson B (2021-02-26). "A novel d-xylose isomerase from the gut of the wood feeding beetle Odontotaenius disjunctus efficiently expressed in Saccharomyces cerevisiae". Scientific Reports. 11 (1): 4766. Bibcode:2021NatSR..11.4766S. doi:10.1038/s41598-021-83937-z. hdl: 1822/72966 . ISSN   2045-2322. PMC   7910561 . PMID   33637780.
  21. 1 2 3 4 5 6 7 Benardout M, Le Gresley A, ElShaer A, Wren SP (February 2022). "Fructose malabsorption: causes, diagnosis and treatment". Br J Nutr. 127 (4): 481–489. doi: 10.1017/S0007114521001215 . PMID   33818329. Creative Commons by small.svg  This article incorporates textfrom this source, which is available under the CC BY 4.0 license.
  22. 1 2 3 Fernández-Bañares F (May 2022). "Carbohydrate Maldigestion and Intolerance". Nutrients. 14 (9): 1923. doi: 10.3390/nu14091923 . PMC   9099680 . PMID   35565890. Creative Commons by small.svg  This article incorporates textfrom this source, which is available under the CC BY 4.0 license.
  23. ↑ Varayil JE, Bauer BA, Hurt RT (2014). "Over-the-Counter Enzyme Supplements: What a Clinician Needs to Know". Concise Review for Clinicians. 89 (9): 980–987. doi: 10.1111/apt.12057 . PMID   23002720. S2CID   6047336.
  24. 1 2 Singh RS, Singh T, Pandey A (2019). "Microbial Enzymes—An Overview". Advances in Enzyme Technology. pp. 1–40. doi:10.1016/B978-0-444-64114-4.00001-7. ISBN   978-0-444-64114-4.
  25. ↑ Komericki P, Akkilic-Materna M, Strimitzer T, Weyermair K, Hammer H, Aberer W (2012). "Oral xylose isomerase decreases breath hydrogen excretion and improves gastrointestinal symptoms in fructose malabsorption — a double-blind, placebo-controlled study". Alimentary Pharmacology & Therapeutics. 36 (10): 980–987. doi: 10.1111/apt.12057 . PMID   23002720. S2CID   6047336.

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