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	PROSITE documentation PDOC00156 [for PROSITE entry PS51415]

Xylose isomerase family profile

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:

Jenkins J.

Last update:

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

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

XYLOSE_ISOMERASE, PS51415; Xylose isomerase family profile  (MATRIX)

• Sequences in UniProtKB/Swiss-Prot known to belong to this class: 196
  • detected by PS51415: 196 (true positives)
  • undetected by PS51415: 0 (false negative or 'partial')
• Other sequence(s) in UniProtKB/Swiss-Prot detected by PS51415:
  NONE.
• Domain architecture view of Swiss-Prot proteins matching PS51415
  
• Retrieve an alignment of UniProtKB/Swiss-Prot true positive hits:
  Clustal format, color, condensed view  /  Clustal format, color  /  Clustal format, plain text  /  Fasta format
• Retrieve the sequence logo from the alignment
• Taxonomic distribution of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51415
• Retrieve a list of all UniProtKB (Swiss-Prot + TrEMBL) entries matching PS51415
• Scan UniProtKB (Swiss-Prot and/or TrEMBL) entries against PS51415
• View ligand binding statistics of PS51415
• Matching PDB structures: 1A0C 1A0D 1A0E 1BHW ... [ALL]

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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