Xylose isomerase

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xylose isomerase
D-Xylose isomerase tetramer from Streptomyces rubiginosus PDB 2glk.[1] One monomer is coloured by secondary structure to highlight the TIM barrel architecture.
EC no.
CAS no.9023-82-9
IntEnzIntEnz view
ExPASyNiceZyme view
MetaCycmetabolic pathway
PDB structuresRCSB PDB PDBe PDBsum
Gene OntologyAmiGO / QuickGO

In enzymology, a xylose isomerase (EC 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]


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 


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]


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[edit]

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
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
mechanism of xylose isomerization

Application in industry[edit]

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 

  • enzymatic degradation of the starch using α-amylase. Also known as liquification.
  • further degradation using glucoamylase and a debranching enzyme.
  • Production of fructose using xylose isomerase

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[edit]

Conversion of glucose to fructose by xylose isomerase
The conversion of glucose to fructose by xylose isomerase. Image taken from doi:10.1017/S0007114521001215[21] 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]


  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. ^ a b c 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. ^ a b c d e f g Wong DW (1995). Food Enzymes Structure and Mechanism. Boston, MA: Springer US. ISBN 978-1-4757-2349-6.
  8. ^ a b 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. ^ a b c 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.
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  16. ^ Nam KH (2022). "Glucose Isomerase: Functions, Structures, and Applications". Applied Sciences. 12: 428. doi:10.3390/app12010428. This article incorporates text from 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. ^ a b c d e f g 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. This article incorporates text from this source, which is available under the CC BY 4.0 license.
  22. ^ a b c Fernández-Bañares F (May 2022). "Carbohydrate Maldigestion and Intolerance". Nutrients. 14 (9): 1923. doi:10.3390/nu14091923. PMC 9099680. PMID 35565890. This article incorporates text from 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. ^ a b 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.

Further reading[edit]

  • Hochster RM, Watson RW (1954). "Enzymatic isomerization of D-xylose to D-xylulose". Arch. Biochem. Biophys. 48 (1): 120–9. doi:10.1016/0003-9861(54)90313-6. PMID 13125579.
  • Slein MW (1955). "Xylose isomerase from Pasteurella pestis, strain A-1122". J. Am. Chem. Soc. 77 (6): 1663–1667. doi:10.1021/ja01611a074.
  • Yamanaka K (1968). "Purification, crystallization and properties of the D-xylose isomerase from Lactobacillus brevis". Biochimica et Biophysica Acta (BBA) - Enzymology. 151 (3): 670–80. doi:10.1016/0005-2744(68)90015-6. PMID 5646045.