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InterPro: IPR001998 Xylose isomerase

Protein matches Help

UniProtKB

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664 proteins

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Detailed:	sorted by AC,	sorted by name,	of known structure	proteins with splice variants
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Architectures
Accession List
Matches in BioMart

Accession

IPR001998 Xylose_isomerase

Type

Family

Signatures Help

Database	ID	Name	Proteins
HAMAP	MF_00455	Xylose_isom_A	499
PRINTS	PR00688	XYLOSISMRASE	610
PROSITE profile	PS51415	XYLOSE_ISOMERASE	662
Signatures in BioMart

InterPro Relationships Help

Parent

IPR012307 Xylose isomerase, TIM barrel domain

Children

IPR013452 Xylose isomerase, bacterial type
IPR013453 Xylose isomerase, actinobacteria

GO Term annotation Help

Process

GO:0005975 carbohydrate metabolic process

Function

GO:0009045 xylose isomerase activity

InterPro annotation

Entry Details in BioMart

Abstract

Xylose isomerase (EC:5.3.1.5) [1] is an enzyme found in microorganisms which catalyzes the interconversion of D-xylose to D-xylulose. It can also isomerize D-ribose to D-ribulose and D-glucose to D-fructose. The enzyme is a homotetramer, which is stabilised by cobalt, and requires magnesium for its catalytic activity. Each subunit contains 2 domains: the core domain is a parallel alpha-beta barrel; the C-terminal domain is a loop structure consisting of 5 helices and is involved in intermolecular contacts between adjacent subunits [2]. The active site lies in a deep pocket near the C-terminal ends of the strands of the barrel domain and includes residues from a second subunit. The tetramer is effectively a dimer of "active" dimers, the active sites being composed of residues from both subunits [2].

Xylose isomerase also exists in plants [3] where it is homodimeric and is manganese-dependent.

Structural links Help

PDB - click here

SCOP: c.1.15.3

CATH: 3.20.20.150

Database links Help

PDBe-motif: PS00172 , PS00173

Enzyme: EC:5.3.1.5

PROSITE doc: PDOC00156

Blocks: IPB001998

CluSTr: ALLvsALL:36286:116.5

PRIAM: PRI001793

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR001998

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

P12070 Xylose isomerase

Q40082 Xylose isomerase

Q9FKK7 Xylose isomerase

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR001998	Xylose isomerase
IPR013453	Xylose isomerase, actinobacteria
IPR013452	Xylose isomerase, bacterial type
IPR012307	Xylose isomerase, TIM barrel domain
IPR013022	Xylose isomerase-like, TIM barrel domain
	SWISS-MODEL
	PDB Chain
	ModBase
	CATH Domain
	SCOP Domain

Publications Open in usermanual
1.	Dauter Z, Dauter M, Hemker J, Witzel H, Wilson KS. Crystallisation and preliminary analysis of glucose isomerase from Streptomyces albus. FEBS Lett. 247 1-8 1989 [PubMed: 2651156] http://dx.doi.org/10.1016/0014-5793(89)81227-X
2.	Henrick K, Collyer CA, Blow DM. 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. J. Mol. Biol. 208 129-57 1989 [PubMed: 2769749] http://dx.doi.org/10.1016/0022-2836(89)90092-2
3.	Kristo P, Saarelainen R, Fagerstrom R, Aho S, Korhola M. Protein purification, and cloning and characterization of the cDNA and gene for xylose isomerase of barley. Eur. J. Biochem. 237 240-6 1996 [PubMed: 8620879] http://dx.doi.org/10.1111/j.1432-1033.1996.0240n.x

Additional Reading Open in usermanual
	Mueller-Dieckmann C, Panjikar S, Schmidt A, Mueller S, Kuper J, Geerlof A, Wilmanns M, Singh RK, Tucker PA, Weiss MS. On the routine use of soft X-rays in macromolecular crystallography. Part IV. Efficient determination of anomalous substructures in biomacromolecules using longer X-ray wavelengths. Acta Crystallogr. D Biol. Crystallogr. 63 2007 366-80 [PubMed: 17327674] http://dx.doi.org/10.1107/S0907444906055624
	Ramagopal UA, Dauter M, Dauter Z. SAD manganese in two crystal forms of glucose isomerase. Acta Crystallogr. D Biol. Crystallogr. 59 2003 868-75 [PubMed: 12777803] http://dx.doi.org/10.1107/S0907444903005663
	Evans G, Bricogne G. Triiodide derivatization and combinatorial counter-ion replacement: two methods for enhancing phasing signal using laboratory Cu Kalpha X-ray equipment. Acta Crystallogr. D Biol. Crystallogr. 58 2002 976-91 [PubMed: 12037300] http://dx.doi.org/10.1107/S0907444902005486
	Vangrysperre W, Ampe C, Kersters-Hilderson H, Tempst P. Single active-site histidine in D-xylose isomerase from Streptomyces violaceoruber. Identification by chemical derivatization and peptide mapping. Biochem. J. 263 1989 195-9 [PubMed: 2604694] http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=EBI&pubmedid=2604694
	Katz AK, Li X, Carrell HL, Hanson BL, Langan P, Coates L, Schoenborn BP, Glusker JP, Bunick GJ. Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction. Proc. Natl. Acad. Sci. U.S.A. 103 2006 8342-7 [PubMed: 16707576] http://dx.doi.org/10.1073/pnas.0602598103
	Fenn TD, Ringe D, Petsko GA. Xylose isomerase in substrate and inhibitor michaelis states: atomic resolution studies of a metal-mediated hydride shift. Biochemistry 43 2004 6464-74 [PubMed: 15157080] http://dx.doi.org/10.1021/bi049812o

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