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Information on EC 5.3.1.5 - xylose isomerase and Organism(s) Streptomyces rubiginosus and UniProt Accession P24300

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IUBMB Comments
Contains two divalent metal ions, preferably magnesium, located at different metal-binding sites within the active site. The enzyme catalyses the interconversion of aldose and ketose sugars with broad substrate specificity. The enzyme binds the closed form of its sugar substrate (in the case of glucose, only the alpha anomer) and catalyses ring opening to generate a form of open-chain conformation that is coordinated to one of the metal sites. Isomerization proceeds via a hydride-shift mechanism.
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Streptomyces rubiginosus
UNIPROT: P24300
Word Map
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
The taxonomic range for the selected organisms is: Streptomyces rubiginosus
Reaction Schemes
Synonyms
D-XI, D-Xylose isomerase, D-Xylose ketoisomerase, D-xylose ketol isomerase, D-xylose ketol-isomerase, D-xylose: ketol-isomerase, D-xylulose keto-isomerase, glucose isomerase, glucose/xylose isomerase, GXI, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-Xylose isomerase
D-Xylose ketoisomerase
-
-
-
-
D-xylose ketol-isomerase
1580
-
D-xylulose keto-isomerase
-
-
-
-
glucose isomerase
1580
-
Isomerase, xylose
-
-
-
-
Optisweet
Spezyme
1580
Finnsugar
Swetase
-
-
-
-
xylose isomerase
1580
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
-
-
SYSTEMATIC NAME
IUBMB Comments
D-xylose aldose-ketose-isomerase
Contains two divalent metal ions, preferably magnesium, located at different metal-binding sites within the active site. The enzyme catalyses the interconversion of aldose and ketose sugars with broad substrate specificity. The enzyme binds the closed form of its sugar substrate (in the case of glucose, only the alpha anomer) and catalyses ring opening to generate a form of open-chain conformation that is coordinated to one of the metal sites. Isomerization proceeds via a hydride-shift mechanism.
CAS REGISTRY NUMBER
COMMENTARY hide
9023-82-9
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
alpha-D-glucose
alpha-D-fructose
show the reaction diagram
-
-
-
-
r
D-glyceraldehyde
dihydroxyacetone
show the reaction diagram
-
-
-
-
?
D-Xylose
D-Xylulose
show the reaction diagram
-
-
-
-
r
D-Glucose
D-Fructose
show the reaction diagram
D-Xylose
D-Xylulose
show the reaction diagram
L-Arabinose
L-Ribulose
show the reaction diagram
low reaction efficiency
-
-
r
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
D-Xylose
D-Xylulose
show the reaction diagram
-
-
-
-
r
D-Xylose
D-Xylulose
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
activates
Fe2+
-
activates
Mn2+
-
activates
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
D-glyceraldehyde
-
competitive inhibition of the isomerization of D-xylose
D-Threonohydroxamic acid
-
competitive inhibitor, complete inhibition at 0.5 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3
D-glyceraldehyde
-
in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25C
4.9
D-xylose
-
in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25C
160 - 340
D-glucose
1 - 548
D-xylose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0001
D-glyceraldehyde
-
in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25C
2.4
D-xylose
-
in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25C
0.03 - 9.22
D-glucose
0.007 - 5.52
D-xylose
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.000034
D-glyceraldehyde
-
in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25C
0.49
D-xylose
-
in D2O, 24 mM imidazole buffer, 10 mM MgCl2, at pH 7.5 and 25C
0.00013 - 1.84
D-xylose
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8 - 8.2
-
in presence of Mg2+ and Co2+, mutants D65A and D163N/E167Q
8
-
in presence of Co2+, mutant E221A; in presence of Mg2+ and Co2+, mutants E221A and D56N
8.1 - 8.3
-
in presence of Mg2+ and Co2+, mutant D81A
8.5
-
in presence of Mg2+ and Co2+, wild-type
8.8
-
in presence of Co2+, wild-type
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
Sequence
XYLA_STRRU
388
0
43227
Swiss-Prot
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
160000
-
neutron diffraction
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homotetramer
-
x-ray crystallography
tetramer
CRYSTALLIZATION/commentary
ORGANISM
UNIPROT
LITERATURE
in complex with D-glyceraldehyde, hanging drop vapor diffusion method, using 0.2-0.3 M Mg-formate at pH 7.0 and 22C
-
structure of E186Q mutant with cyclic glucose bound at the active site, to 2.2 A resolution. Residue His54 is doubly protonated and is poised to protonate the glucose O5 position, while Lys289, which is neutral, promotes deprotonation of the glucose O1H hydroxyl group via an activated water molecule. An extended hydrogen-bonding network connects the conserved residues Lys289 and Lys183 through three structurally conserved water molecules and residue 186
-
the mechanism of ring-opening for L-arabinose is the same as for the reaction with D-xylose. In the reactive Michaelis complex L-arabinose is distorted to the high-energy 5S1 conformation. Amino acid substitutions in a hydrophobic pocket near C5 of L-arabinose can enhance sugar binding. L-ribulose and L-ribose are found in furanose forms when bound to the enzyme
-
analysis of the location of hydrogen atoms by time-of-flight neutron Laue technique. The neutron structure of crystalline XI with bound product, D-xylulose, shows, that O5 of D-xylulose is not protonated but is hydrogen-bonded to doubly protonated His54. Also, Lys289, which is neutral in native XI, is protonated, while the catalytic water in native XI has become activated to a hydroxyl anion which is in the proximity of C1 and C2, the molecular site of isomerization of xylose
-
cooling crystallization from 0.17 M MgSO4 solution
-
neutron diffraction, largest crystals at 18C, 95 mg/ml xylose isomerase, 16.9% ammonium sulfate, mathematical analysis to determine optimal conditions for crystallization
-
neutron quasi-Laue diffraction, resolution: 2.2 A - clear visibility of deuterium atoms, clarification of critical residues at the active site and their protonation states
-
study on the dynamics of solute transport in orthorhombic D-xylose isomerase crystals by means of Brownian dynamics and molecular dynamics simulations and investigation of the diffusion of S-phenylglycine molecules inside XI crystals. The S-phenylglycine molecules mostly interact with residues His54, Asp287, and Lys183. In general, the diffusivities of solute species are found to be 1 to 2 orders of magnitude lower than those of the corresponding free molecules in water
-
time-of-flight neutron diffraction at 1.8 A resolution, metal-free enzyme - emphasis on the active site of xylose isomerase, especially of protonation states of His, Lys and H2O
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E186Q
-
crystallization data
D163N/E167Q
-
40-60% of wild-type activity, lower pH optimum than wild-type, nearly same tehrmostability as wild-type
D287N
-
inactive
D56N
-
turnover number increased by 30-40% over that ofwild-type at pH 7.3, lower pH optimum than wild-type, nearly same thermostability as wild-type
D65A
-
40-60% of wild-type activity, lower pH optimum than wild-type, nearly same tehrmostability as wild-type
D81A
-
40-60% of wild-type activity, lower pH optimum than wild-type, nearly same tehrmostability as wild-type
E221A
-
turnover number increased by 30-40% over that from wild-type at pH 7.3, lower pH optimum than wild-type, nearly same tehrmostability as wild-type
H220S
-
decreased affinity for Mg2+ and decraesed activity in contrast to wild-type
N185K
-
decreased affinity for Mg2+ and decraesed activity in contrast to wild-type
ORGANIC SOLVENT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Acetone
-
70-80% of cross-linked crystalline xylose isomerase activity is left after incubation for 24 h at 50C in buffer solutions (pH 7.2) containing 10-90% acetone. Soluble xylose isomerase is considerably less stable in acetone-containing solutions. The addition of acetone enhances the production of fructose from glucose by enhancing the reaction rate and shifting the equilibrium toward fructose. However, xylose isomerase must be in the form of cross-linked crystals for maximal activity and stability
Ethanol
-
in buffer containing 50% ethanol only 2% of the initial cross-linked crystalline xylose isomerase activity is retained after 24 h at 50C. Soluble xylose isomerase is considerably less stable in ethanol-containing solutions
Methanol
-
cross-linked crystalline xylose isomerase is inactivated in 24 h at 50C even more in maleate buffer containing 50% methanol
Pyridine
-
cross-linked crystalline xylose isomerase is inactivated in 24 h at 50C even more in maleate buffer containing 10% pyridine
PURIFICATION/commentary
ORGANISM
UNIPROT
LITERATURE
from a stock solution of a food grade product, 2 counterdiffusion dialysis devices: diffusion-controlled apparatus for microgravity and counterdiffusion cell, growth of crystals approx. 3 months
-
gel filtration over Sephacryl S200 - dialysis against 0.05 g/l MgSO4, purity control verified with capillary electrophoresis
-
gel filtration with Sephacryl S-200 high resolution media, running buffer composed of 0.05 M sodium phosphate pH 7.7, 0.1 M sodium chloride and 0.02% azide - final purity of xylose isomerase: 96%
-
HisTrap crude nickel affinity column chromatography
-
CLONED/commentary
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
-
expression in Escherichia coli
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
nutrition
-
high fructose corn syrups
synthesis
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Carrell, H.L.; Rubin, B.H.; Hurley, T.J.; Glusker, J.P.
X-ray crystal structure of D-xylose isomerase at 4-A resolution
J. Biol. Chem.
259
3230-3236
1984
Streptomyces rubiginosus
Manually annotated by BRENDA team
Bhosale, S.H.; Rao, M.B.; Deshpande, V.V.
Molecular industrial aspects of glucose isomerase
Microbiol. Rev.
60
280-300
1996
Actinomyces olivocinereus, Actinoplanes missouriensis, Actinoplanes sp., Aerobacter levanicum, Aeromonas hydrophila, Arthrobacter sp., Bacillus coagulans, Bacillus licheniformis, Bacillus megaterium, Brevibacterium helvolum, Brevibacterium pentosoaminoacidicum, Citrobacter freundii, Citrobacter intermedius, Corynebacterium sp., Desemzia incerta, Enterobacter cloacae, Escherichia coli, Gordonia rubripertincta, Klebsiella aerogenes, Lactobacillus buchneri, Lactobacillus fermentum, Lactobacillus gayonii, Lactobacillus lycopersici, Lactobacillus mannitopoeus, Lactobacillus pentosus, Lactobacillus plantarum, Leuconostoc mesenteroides, Microbacterium arborescens, Microbispora rosea, Micromonospora coerulea, Mycobacterium sp., Nocardia asteroides, Nocardiopsis dassonvillei, Paracolobacterium aerogenoides, Pseudonocardia sp., Sarcina sp., Sphingomonas paucimobilis, Streptococcus venuceus, Streptomyces achromogenes, Streptomyces bikiniensis, Streptomyces bobili, Streptomyces californicus, Streptomyces cinnamonensis, Streptomyces echinatus, Streptomyces flaveus, Streptomyces flavovirens, Streptomyces fradiae, Streptomyces glaucescens, Streptomyces griseofuscus, Streptomyces griseolus, Streptomyces griseus, Streptomyces matensis, Streptomyces nivens, Streptomyces olivaceus, Streptomyces olivochromogenes, Streptomyces phaeochromogenes, Streptomyces platensis, Streptomyces roseochromogenes, Streptomyces rubiginosus, Streptomyces venezuelae, Streptomyces virginiae, Streptomyces wedmorensis, Streptosporangium album, Streptosporangium vulgare, Thermoanaerobacterium thermosulfurigenes, Thermoanaerobacter thermohydrosulfuricus, Thermopolyspora sp., Thermus thermophilus, Xanthomonas sp., Zymomonas mobilis
Manually annotated by BRENDA team
Vuolanto, A.; Uotila, S.; Leisola, M.; Visuri, K.
Solubility and crystallization of xylose isomerase from Streptomyces rubiginosus
J. Crystal Growth
257
403-411
2003
Streptomyces rubiginosus
-
Manually annotated by BRENDA team
Cha, J.
Contribution of second metal binding site for metal specificity of D-xylose isomerase
J. Microbiol. Biotechnol.
9
757-763
1999
Streptomyces rubiginosus
-
Manually annotated by BRENDA team
Cha, J.; Batt, C.A.
Lowering the pH optimum of D-xylose isomerase: the effect of mutations of the negatively charged residues
Mol. Cells
8
374-382
1998
Streptomyces rubiginosus
Manually annotated by BRENDA team
Straatsma, J.; Vellenga, K.; Witt, H.G.J.de; Joosten, G.E.
Isomerization of glucose to fructose. 2. Optimization of reaction conditions in the production of high fructose syrup by isomerization of glucose catalyzed by a whole cell immobilized glucose isomerase catalyst
Ind. Eng. Chem. Process Des. Dev.
22
356-361
1983
Actinoplanes missouriensis, Bacillus coagulans, Streptomyces phaeochromogenes, Streptomyces rubiginosus
-
Manually annotated by BRENDA team
Hanson, B.L.; Langan, P.; Katz, A.K.; Li, X.; Harp, J.M.; Glusker, J.P.; Schoenborn, B.P.; Bunick, G.J.
A preliminary time-of-flight neutron diffraction study of Streptomyces rubiginosus D-xylose isomerase
Acta Crystallogr. Sect. D
60
241-249
2004
Streptomyces rubiginosus
Manually annotated by BRENDA team
Vilonen, K.M.; Vuolanto, A.; Jokela, J.; Leisola, M.S.; Krause, A.O.
Enhanced glucose to fructose conversion in acetone with xylose isomerase stabilized by crystallization and cross-linking
Biotechnol. Prog.
20
1555-1560
2004
Streptomyces rubiginosus
Manually annotated by BRENDA team
Karimaki, J.; Parkkinen, T.; Santa, H.; Pastinen, O.; Leisola, M.; Rouvinen, J.; Turunen, O.
Engineering the substrate specificity of xylose isomerase
Protein Eng. Des. Sel.
17
861-869
2004
Actinoplanes missouriensis, Streptomyces rubiginosus (P24300), Streptomyces rubiginosus
Manually annotated by BRENDA team
Meilleur, F.; Snell, E.H.; van der Woerd, M.J.; Judge, R.A.; Myles, D.A.
A quasi-Laue neutron crystallographic study of D-xylose isomerase
Eur. Biophys. J.
35
601-609
2006
Streptomyces rubiginosus
Manually annotated by BRENDA team
Snell, E.H.; van der Woerd, M.J.; Damon, M.; Judge, R.A.; Myles, D.A.; Meilleur, F.
Optimizing crystal volume for neutron diffraction: D-xylose isomerase
Eur. Biophys. J.
35
621-632
2006
Streptomyces rubiginosus
Manually annotated by BRENDA team
Katz, A.K.; Li, X.; Carrell, H.L.; Hanson, B.L.; Langan, P.; Coates, L.; Schoenborn, B.P.; Glusker, J.P.; Bunick, G.J.
Locating active-site hydrogen atoms in D-xylose isomerase: time-of-flight neutron diffraction
Proc. Natl. Acad. Sci. USA
103
8342-8347
2006
Streptomyces rubiginosus (P24300), Streptomyces rubiginosus
Manually annotated by BRENDA team
Kovalevsky, A.Y.; Katz, A.K.; Carrell, H.L.; Hanson, L.; Mustyakimov, M.; Fisher, S.Z.; Coates, L.; Schoenborn, B.P.; Bunick, G.J.; Glusker, J.P.; Langan, P.
Hydrogen location in stages of an enzyme-catalyzed reaction: time-of-flight neutron structure of D-xylose isomerase with bound D-xylulose
Biochemistry
47
7595-7597
2008
Streptomyces rubiginosus (P24300)
Manually annotated by BRENDA team
Malek, K.; Coppens, M.O.
Molecular simulations of solute transport in xylose isomerase crystals
J. Phys. Chem. B
112
1549-1554
2008
Streptomyces rubiginosus (P24300)
Manually annotated by BRENDA team
Kovalevsky, A.Y.; Hanson, L.; Fisher, S.Z.; Mustyakimov, M.; Mason, S.A.; Forsyth, V.T.; Blakeley, M.P.; Keen, D.A.; Wagner, T.; Carrell, H.L.; Katz, A.K.; Glusker, J.P.; Langan, P.
Metal ion roles and the movement of hydrogen during reaction catalyzed by D-xylose isomerase: a joint x-ray and neutron diffraction study
Structure
18
688-699
2010
Streptomyces rubiginosus (P24300)
Manually annotated by BRENDA team
Toteva, M.M.; Silvaggi, N.R.; Allen, K.N.; Richard, J.P.
Binding energy and catalysis by D-xylose isomerase: kinetic, product, and X-ray crystallographic analysis of enzyme-catalyzed isomerization of (R)-glyceraldehyde
Biochemistry
50
10170-10181
2011
Streptomyces rubiginosus (P24300)
Manually annotated by BRENDA team
Waltman, M.; Yang, Z.; Langan, P.; Graham, D.; Kovalevsky, A.
Engineering acidic Streptomyces rubiginosus D-xylose isomerase by rational enzyme design
Protein Eng.
27
59-64
2014
Streptomyces rubiginosus
Manually annotated by BRENDA team
Munshi, P.; Snell, E.H.; van der Woerd, M.J.; Judge, R.A.; Myles, D.A.; Ren, Z.; Meilleur, F.
Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant
Acta Crystallogr. Sect. D
70
414-420
2014
Streptomyces rubiginosus (P24300)
Manually annotated by BRENDA team
Langan, P.; Sangha, A.K.; Wymore, T.; Parks, J.M.; Yang, Z.K.; Hanson, B.L.; Fisher, Z.; Mason, S.A.; Blakeley, M.P.; Forsyth, V.T.; Glusker, J.P.; Carrell, H.L.; Smith, J.C.; Keen, D.A.; Graham, D.E.; Kovalevsky, A.
L-Arabinose binding, isomerization, and epimerization by D-xylose isomerase X-ray/neutron crystallographic and molecular simulation study
Structure
22
1287-1300
2014
Streptomyces rubiginosus (P24300)
Manually annotated by BRENDA team
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