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Information on EC 5.3.1.5 - xylose isomerase and Organism(s) Thermus thermophilus and UniProt Accession P26997

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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 xylose and 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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Thermus thermophilus
UNIPROT: P26997
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The taxonomic range for the selected organisms is: Thermus thermophilus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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alpha-D-xylopyranose
=
alpha-D-xylufuranose
=
alpha-D-xylufuranose
Synonyms
xylose isomerase, glucose isomerase, d-xylose isomerase, spezyme, xylose (glucose) isomerase, glucose/xylose isomerase, sdxyi, tthxi, tcaxi, sweetzyme, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-xylose: ketol-isomerase
-
D-xylose aldose-ketose-isomerase
-
-
-
-
D-xylose isomerase
-
-
-
-
D-Xylose ketoisomerase
-
-
-
-
D-xylose ketol isomerase
-
-
D-xylulose keto-isomerase
-
-
-
-
Isomerase, xylose
-
-
-
-
Swetase
-
-
-
-
xylose isomerase
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
isomerization
-
-
SYSTEMATIC NAME
IUBMB Comments
alpha-D-xylopyranose 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 xylose and glucose, only the alpha anomer [4]) 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
D-fructose
D-mannose
show the reaction diagram
-
-
-
r
D-Glucose
D-Fructose
show the reaction diagram
-
-
-
r
D-Lyxose
D-Xylulose
show the reaction diagram
-
-
-
r
D-Mannose
D-Fructose
show the reaction diagram
-
-
-
r
D-Xylose
D-Xylulose
show the reaction diagram
L-arabinose
L-ribulose
show the reaction diagram
-
-
-
r
L-ribulose
L-ribose
show the reaction diagram
-
-
-
r
D-Glucose
D-Fructose
show the reaction diagram
D-Xylose
D-Xylulose
show the reaction diagram
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
D-Xylose
D-Xylulose
show the reaction diagram
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Mn2+
maximal activity with 1 mM Mn2+
additional information
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Co2+
about 58% residual activity at 1 mM
Cu2+
less than 10% residual activity at 1 mM
Mg2+
about 35% residual activity at 1 mM
Ni2+
less than 5% residual activity at 1 mM
Zn2+
complete inhibition at 1 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
215
D-Lyxose
mutant enzyme D256R, at pH 7.0 and 85°C
185 - 1005
D-mannose
11.7 - 605
D-xylose
138 - 1450
L-arabinose
52 - 171.8
D-glucose
3.44 - 89.4
D-xylose
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
25 - 38
D-Lyxose
2 - 18
D-mannose
50.7 - 160.5
D-xylose
6.5 - 13
L-arabinose
0.7 - 88.7
D-glucose
46.6 - 258
D-xylose
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.041 - 0.17
D-Lyxose
0.017 - 0.15
D-mannose
2.92 - 9.8
D-xylose
0.008 - 0.09
L-arabinose
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
4.6 - 1174
xylitol
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
132
wild type enzyme, with L-arabinose as substrate, at pH 7.0 and 85°C
273
wild type enzyme, with D-mannose as substrate, at pH 7.0 and 85°C
330
mutant enzyme D256R, with L-arabinose as substrate, at pH 7.0 and 85°C
380
wild type enzyme, with D-lyxose as substrate, at pH 7.0 and 85°C
682
mutant enzyme D256R, with D-mannose as substrate, at pH 7.0 and 85°C
950
mutant enzyme D256R, with D-lyxose as substrate, at pH 7.0 and 85°C
0.04
-
Saccharomyces cerevisiae overexpressing xylose isomerase from Thermus thermophilus, 30°C
1
-
Saccharomyces cerevisiae overexpressing xylose isomerase from Thermus thermophilus, 85°C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
5 - 10
-
mutants E372G/V379A, E372G/F163L and E372G
5 - 8
-
wild-type
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
75
-
mutants E372G/V379A
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 90
temperature profiles of recombinant mutant enzymes, overview
55 - 95
about 52% activity at 55°C, about 65% activity at 60°C, about 75% activity at 65°C, about 78% activity at 70°C, about 85% activity at 75°C, about 95% activity at 80°C, about 78% activity at 90°C, and about 52% activity at 95°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
44000
x * 44000, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 44000, SDS-PAGE
homotetramer
-
alpha4, crystallization studies
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
at room temperature with polyethylene glycol 4000 as precipitant, orthorhombic space group P212121 with a: 73.34 A, b: 144.05 A and c 155.07 A
-
ortjorhombic space group P212121 with a: 73.34 A, b: 144.05 A and c: 155.07 A
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D254R/D256R
complete loss of activity
D256R
the mutant shows an increase in the specificity on D-lyxose, L-arabinose and D-mannose
N91D
site-directed mutagenesis
N91D/D375G
site-directed mutagenesis, the mutant shows increased activity but reduced thermostability compared to the wild-type enzyme
N91D/D375G/V385A
site-directed mutagenesis, the mutant shows increased activity but reduced thermostability compared to the wild-type enzyme
N91D/K355A
site-directed mutagenesis, the mutant shows increased activity but reduced thermostability compared to the wild-type enzyme
N91D/V144A
site-directed mutagenesis, the mutant shows increased activity but reduced thermostability compared to the wild-type enzyme
E372G
-
broader pH range and nine times higher turnover for D-xylose at 60°C than wild-type
E372G/F163L
-
broader pH range and nine times higher turnover for D-xylose at 60°C than wild-type
E372G/V379A
-
broader pH range and nine times higher turnover for D-xylose at 60°C than wild-type
N91D
-
the mutant shows increased substrate specificity for D-xylose compared to the wild type enzyme
additional information
-
Saccharomyces cerevisiae: five enzymes of non-oxidative pentose-phosphate-pathway are induced, a non-specific aldose reductase is deleted
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
pH stability at 85°C is optimal around pH 7.0
746869
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 90
thermostability of recombinant mutant enzymes, overview
85
-
with Mg2+, half-life: 20 h
additional information
-
stability is also strongly influenced by the addition of divalent cations. The addition of Mn2+ gives the highest thermostability, Mg2+ has a smaller stabilizing effect, while other metals have no effect
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
smaller stabilizing effect, while other metals have no effect
-
stability is also strongly influenced by the addition of divalent cations. The addition of Mn2+ gives the highest thermostability, Mg2+ has a
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
Ni-NTA column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
expression of mutant enzymes in Escherichia coli strain BL21 (DE3)
expression in Escherichia coli
-
expression in Escherichia coli HB101
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Saccharomyces cerevisiae is transformed with a gene encoding xylose isomerase (Thermus thermophilus)
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the production of the cloned gene in Escherichia coli and Bacillus brevis are compared expression in Escherichia coli and Bacillus brevis. Bacillus brevis is able to produce the isomerase efficiently (more than 1 g/l)
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
energy production
-
engineering of Saccharomyces cerevisiae for alcoholic fermentation of D-xylose
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
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 licheniformis, Brevibacterium helvolum, Brevibacterium pentosoaminoacidicum, Citrobacter freundii, Citrobacter intermedius, Corynebacterium sp., Desemzia incerta, Enterobacter cloacae, Escherichia coli, Gordonia rubripertincta, Klebsiella aerogenes, Lactiplantibacillus pentosus, Lactiplantibacillus plantarum, Lactobacillus gayonii, Lactobacillus lycopersici, Lactobacillus mannitopoeus, Lentilactobacillus buchneri, Leuconostoc mesenteroides, Limosilactobacillus fermentum, Microbacterium arborescens, Microbispora rosea, Micromonospora coerulea, Mycobacterium sp., Nocardia asteroides, Nocardiopsis dassonvillei, Paracolobacterium aerogenoides, Priestia megaterium, Pseudonocardia sp., Sarcina sp., Sphingomonas paucimobilis, Streptococcus venuceus, Streptomyces achromogenes, Streptomyces bikiniensis, Streptomyces bobili, Streptomyces californicus, 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 roseochromogenus, Streptomyces rubiginosus, Streptomyces venezuelae, Streptomyces virginiae, Streptomyces wedmorensis, Streptosporangium album, Streptosporangium vulgare, Thermoanaerobacter thermohydrosulfuricus, Thermoanaerobacterium thermosulfurigenes, Thermopolyspora sp., Thermus thermophilus, Weizmannia coagulans, Xanthomonas sp., Zymomonas mobilis
Manually annotated by BRENDA team
Lonn, A.; Gardonyi, M.; van Zyl, W.; Hahn-Hagerdal, B.; Otero, R.C.
Cold adaptation of xylose isomerase from Thermus thermophilus through random PCR mutagenesis. Gene cloning and protein characterization
Eur. J. Biochem.
269
157-163
2002
Thermus thermophilus
Manually annotated by BRENDA team
Chang, C.; Park, B.C.; Lee, D.S.; Suh, S.W.
A thermostable xylose isomerase from Thermus thermophilus: biochemical characterization, crystallization, and preliminary X-ray analyses
J. Biochem. Mol. Biol.
31
600-603
1998
Thermus thermophilus
-
Manually annotated by BRENDA team
Chang, C.; Park, B.C.; Lee, D.S.; Suh, S.W.
Crystal structures of thermostable xylose isomerases from Thermus caldophilus and Thermus thermophilus: Possible structural determinants of thermostability
J. Mol. Biol.
288
623-634
1999
Thermus thermophilus, Thermus caldophilus
Manually annotated by BRENDA team
van Maris, A.J.; Winkler, A.A.; Kuyper, M.; de Laat, W.T.; van Dijken, J.P.; Pronk, J.T.
Development of efficient xylose fermentation in Saccharomyces cerevisiae: xylose isomerase as a key component
Adv. Biochem. Eng. Biotechnol.
108
179-204
2007
Thermus thermophilus, no activity in Saccharomyces cerevisiae, Piromyces sp.
Manually annotated by BRENDA team
Xu, W.; Yan, M.; Xu, L.; Ding, L.; Ouyang, P.
Engineering the activity of thermophilic xylose isomerase by site-directed mutation at subunit interfaces
Enzyme Microb. Technol.
44
77-83
2009
Thermus thermophilus (P26997)
-
Manually annotated by BRENDA team
Xu, W.; Shao, R.; Li, Y.; Yan, M.; Ouyang, P.
Study on the substrate specificity of xylose isomerase N91D mutant from Thermus thermophilus HB8 by molecular simulation
Adv. Mater. Res.
236-238
968-973
2011
Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579
-
Manually annotated by BRENDA team
Patel, D.H.; Cho, E.J.; Kim, H.M.; Choi, I.S.; Bae, H.J.
Engineering of the catalytic site of xylose isomerase to enhance bioconversion of a non-preferential substrate
Protein Eng. Des. Sel.
25
331-336
2012
Thermus thermophilus (P26997), Thermus thermophilus, Thermus thermophilus HB8 / ATCC 27634 / DSM 579 (P26997)
Manually annotated by BRENDA team
Dekker, K.; Sugiura, A.; Yamagata, H.; Sakaguchi, K.; Udaka, S.
Efficient production of thermostable Thermus thermophilus xylose isomerase in Escherichia coli and Bacillus brevis
Appl. Microbiol. Biotechnol.
36
727-732
1992
Thermus thermophilus
Manually annotated by BRENDA team