PROSITE documentation PDOC00156
Xylose isomerase family profile


Xylose isomerase (EC [1] is an enzyme found in microorganisms which catalyzes the interconversion of an aldo sugar D-xylose to a keto sugar D-xylulose. It can also isomerize D-ribose to D-ribulose and D-glucose to D-fructose. Xylose isomerase seems to require magnesium for its activity, while cobalt is necessary to stabilize the tetrameric structure of the enzyme.

Xylose isomerase also exists in plants [2] where it is manganese-dependent. The enzyme has also been found in anaerobic fungi [3].

A number of residues are conserved in all known xylose isomerases. A histidine in the N-terminal section of the enzyme has been shown [4] to be involved in the catalytic mechanism of the enzyme. Two glutamate residues, a histidine and four aspartate residues are the metal-binding sites that bind two ions of magnesium, cobalt, or manganese [5,6,7].

Three-dimensional structures of xylose isomerases show a that each subunit contains a common α/β-barrel fold (see <PDB:2GLK; A>) [7] similar to that of other divalent metal-dependent TIM barrel enzymes, such as rhamnose isomerase [8] and endonuclease 4 (see <PDOC00599>) [1,5,6]. The C-terminal smaller part forms an extended helical fold that seems to be implicated in multimerization.

We have developed a profile that covers the entire xylose isomerase structure.

Expert(s) to contact by email:

Jenkins J.

Last update:

February 2009 / Text revised; profile added; patterns deleted.


Technical section

PROSITE method (with tools and information) covered by this documentation:

XYLOSE_ISOMERASE, PS51415; Xylose isomerase family profile  (MATRIX)


1AuthorsDauter Z. Dauter M. Hemker J. Witzel H. Wilson K.S.
TitleCrystallisation and preliminary analysis of glucose isomerase from Streptomyces albus.
SourceFEBS Lett. 247:1-8(1989).
PubMed ID2651156

2AuthorsKristo P.A. Saarelainen R. Fagerstrom R. Aho S. Korhola M.
TitleProtein purification, and cloning and characterization of the cDNA and gene for xylose isomerase of barley.
SourceEur. J. Biochem. 237:240-246(1996).
PubMed ID8620879

3AuthorsHarhangi H.R. Akhmanova A.S. Emmens R. van der Drift C. de Laat W.T. van Dijken J.P. Jetten M.S. Pronk J.T. Op den Camp H.J.
TitleXylose metabolism in the anaerobic fungus Piromyces sp. strain E2 follows the bacterial pathway.
SourceArch. Microbiol. 180:134-141(2003).
PubMed ID12811467

4AuthorsVangrysperre W. Ampe C. Kersters-Hilderson H. Tempst P.
TitleSingle active-site histidine in D-xylose isomerase from Streptomyces violaceoruber. Identification by chemical derivatization and peptide mapping.
SourceBiochem. J. 263:195-199(1989).
PubMed ID2604694

5AuthorsHenrick K. Collyer C.A. Blow D.M.
TitleStructures of D-xylose isomerase from Arthrobacter strain B3728 containing the inhibitors xylitol and D-sorbitol at 2.5 A and 2.3 A resolution, respectively.
SourceJ. Mol. Biol. 208:129-157(1989).
PubMed ID2769749

6AuthorsChang C. Park B.C. Lee D.S. Suh S.W.
TitleCrystal structures of thermostable xylose isomerases from Thermus caldophilus and Thermus thermophilus: possible structural determinants of thermostability.
SourceJ. Mol. Biol. 288:623-634(1999).
PubMed ID10329168

7AuthorsKatz A.K. Li X. Carrell H.L. Hanson B.L. Langan P. Coates L. Schoenborn B.P. Glusker J.P. Bunick G.J.
TitleLocating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction.
SourceProc. Natl. Acad. Sci. U.S.A. 103:8342-8347(2006).
PubMed ID16707576

8AuthorsKorndoerfer I.P. Fessner W.D. Matthews B.W.
TitleThe structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution.
SourceJ. Mol. Biol. 300:917-933(2000).
PubMed ID10891278

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