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InterPro: IPR013022 Xylose isomerase-like, TIM barrel domain

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8189 proteins

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Accession

IPR013022 Xyl_isomerase-like_TIM-brl

Type

Domain

Signatures Help

Database	ID	Name	Proteins
Gene3D	G3DSA:3.20.20.150	Xyl_isomerase-like_TIM-brl	7045
SuperFamily	SSF51658	Xyl_isomerase-like_TIM-brl	8182
Signatures in BioMart

InterPro Relationships Help

Children

IPR012307 Xylose isomerase, TIM barrel domain

Found in

IPR004560 Putative hexulose-6-phosphate isomerase
IPR004601 UV-endonuclease UvdE
IPR004628 Mannonate dehydratase
IPR007801 Protein of unknown function DUF692
IPR009308 Rhamnose isomerase
IPR013451 L-rhamnose catabolism isomerase
IPR013452 Xylose isomerase, bacterial type
IPR013453 Xylose isomerase, actinobacteria
IPR013457 Rhamnose isomerase related
IPR014621 Uncharacterised conserved protein, sugar epimerase domain-containing
IPR017643 Hydroxypyruvate isomerase

Contains

IPR011418 AP endonuclease, family 2, C-terminal
IPR018246 AP endonuclease, family 2, zinc binding site

InterPro annotation

Entry Details in BioMart

Abstract

This entry represents a structural motif with a beta/alpha TIM barrel found in several proteins families:

Endonuclease IV (EC:3.1.21.2), an AP (apurinic/apyrimidinic) endonuclease that primes DNA repair synthesis by cleaving the DNA backbone 5' of AP sites [1].
L-rhamnose isomerase (EC:5.3.1.14), a tetramer of four TIM barrels that catalyses the isomerisation between aldoses and ketoses, such as between L-rhamnose and L-rhamnulose [2].
Xylose isomerase (EC:5.3.1.5), which catalyses the first reaction in the catabolism of D-xylose by converting D-xylose to D-xylulose [3].
Mannonate dehydratase UxuA, which along with mannonate oxidoreductase converts D-fructuronate to 2-keto-3-deoxy-D-gluconate [4].

These proteins share similar, but not identical, metal-binding sites. In addition, xylose isomerase and L-rhamnose isomerase each have additional alpha-helical domains involved in tetramer formation. This entry differs from IPR012307 in having a wider coverage of TIM-barrel protein families.

Structural links Help

PDB - click here

SCOP: c.1.15.1 , c.1.15.2 , c.1.15.3 , c.1.15.4 , c.1.15.5 , c.1.15.6 , c.1.15.7

CATH: 3.20.20.150

Taxonomic coverage Help

Overlapping InterPro entries Help

IPR013022

Numbers of overlapping proteins

Average numbers of overlapping amino acids

Example proteins Help

P22936 DNA-(apurinic or apyrimidinic site) lyase 1

P36951 Putative hydroxypyruvate isomerase

Q10002 DNA-(apurinic or apyrimidinic site) lyase

Q5T013 Putative hydroxypyruvate isomerase

Q8R1F5 Putative hydroxypyruvate isomerase

More proteins

Example Proteins Key

InterPro entry accession number/name and structure databases		Colour code
IPR001719	Endodeoxyribonuclease IV
IPR018246	AP endonuclease, family 2, zinc binding site
IPR012307	Xylose isomerase, TIM barrel domain
IPR013022	Xylose isomerase-like, TIM barrel domain
	SWISS-MODEL
	ModBase

Publications Open in usermanual
1.	Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98 397-408 1999 [PubMed: 10458614] http://dx.doi.org/10.1016/S0092-8674(00)81968-6
2.	Yoshida H, Yamada M, Ohyama Y, Takada G, Izumori K, Kamitori S. The structures of L-rhamnose isomerase from Pseudomonas stutzeri in complexes with L-rhamnose and D-allose provide insights into broad substrate specificity. J. Mol. Biol. 365 1505-16 2007 [PubMed: 17141803] http://dx.doi.org/10.1016/j.jmb.2006.11.004
3.	Meilleur F, Snell EH, van der Woerd MJ, Judge RA, Myles DA. A quasi-Laue neutron crystallographic study of D-xylose isomerase. Eur. Biophys. J. 35 601-9 2006 [PubMed: 16673077] http://dx.doi.org/10.1007/s00249-006-0066-6
4.	Robert-Baudouy J, Portalier R, Stoeber F. Regulation of hexuronate system genes in Escherichia coli K-12: multiple regulation of the uxu operon by exuR and uxuR gene products. J. Bacteriol. 145 211-20 1981 [PubMed: 7007313] http://ukpmc.ac.uk/articlerender.cgi?tool=EBI&pubmedid=7007313

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
	Garcin ED, Hosfield DJ, Desai SA, Haas BJ, Bjoras M, Cunningham RP, Tainer JA. DNA apurinic-apyrimidinic site binding and excision by endonuclease IV. Nat. Struct. Mol. Biol. 15 2008 515-22 [PubMed: 18408731] http://dx.doi.org/10.1038/nsmb.1414
	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
	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

InterPro 23.1