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PROSITE documentation PDOC00156Xylose isomerase family profile
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PURL: https://purl.expasy.org/prosite/documentation/PDOC00156
Xylose isomerase (EC 5.3.1.5) [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: Last update:February 2009 / Text revised; profile added; patterns deleted.
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PROSITE method (with tools and information) covered by this documentation:
| 1 | Authors | Dauter Z. Dauter M. Hemker J. Witzel H. Wilson K.S. |
| Title | Crystallisation and preliminary analysis of glucose isomerase from Streptomyces albus. | |
| Source | FEBS Lett. 247:1-8(1989). | |
| PubMed ID | 2651156 |
| 2 | Authors | Kristo P.A. Saarelainen R. Fagerstrom R. Aho S. Korhola M. |
| Title | Protein purification, and cloning and characterization of the cDNA and gene for xylose isomerase of barley. | |
| Source | Eur. J. Biochem. 237:240-246(1996). | |
| PubMed ID | 8620879 |
| 3 | Authors | Harhangi 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. |
| Title | Xylose metabolism in the anaerobic fungus Piromyces sp. strain E2 follows the bacterial pathway. | |
| Source | Arch. Microbiol. 180:134-141(2003). | |
| PubMed ID | 12811467 | |
| DOI | 10.1007/s00203-003-0565-0 |
| 4 | Authors | Vangrysperre W. Ampe C. Kersters-Hilderson H. Tempst P. |
| Title | Single active-site histidine in D-xylose isomerase from Streptomyces violaceoruber. Identification by chemical derivatization and peptide mapping. | |
| Source | Biochem. J. 263:195-199(1989). | |
| PubMed ID | 2604694 |
| 5 | Authors | Henrick K. Collyer C.A. Blow D.M. |
| Title | Structures 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. | |
| Source | J. Mol. Biol. 208:129-157(1989). | |
| PubMed ID | 2769749 |
| 6 | Authors | Chang C. Park B.C. Lee D.S. Suh S.W. |
| Title | Crystal structures of thermostable xylose isomerases from Thermus caldophilus and Thermus thermophilus: possible structural determinants of thermostability. | |
| Source | J. Mol. Biol. 288:623-634(1999). | |
| PubMed ID | 10329168 | |
| DOI | 10.1006/jmbi.1999.2696 |
| 7 | Authors | Katz A.K. Li X. Carrell H.L. Hanson B.L. Langan P. Coates L. Schoenborn B.P. Glusker J.P. Bunick G.J. |
| Title | Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction. | |
| Source | Proc. Natl. Acad. Sci. U.S.A. 103:8342-8347(2006). | |
| PubMed ID | 16707576 | |
| DOI | 10.1073/pnas.0602598103 |
| 8 | Authors | Korndoerfer I.P. Fessner W.D. Matthews B.W. |
| Title | The structure of rhamnose isomerase from Escherichia coli and its relation with xylose isomerase illustrates a change between inter and intra-subunit complementation during evolution. | |
| Source | J. Mol. Biol. 300:917-933(2000). | |
| PubMed ID | 10891278 | |
| DOI | 10.1006/jmbi.2000.3896 |
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