Information on EC 3.2.1.177 - alpha-D-xyloside xylohydrolase

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The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea

EC NUMBER
COMMENTARY hide
3.2.1.177
-
RECOMMENDED NAME
GeneOntology No.
alpha-D-xyloside xylohydrolase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Hydrolysis of terminal, non-reducing alpha-D-xylose residues with release of alpha-D-xylose.
show the reaction diagram
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-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
xyloglucan degradation II (exoglucanase)
-
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non-pathway related
-
-
SYSTEMATIC NAME
IUBMB Comments
alpha-D-xyloside xylohydrolase
The enzyme catalyses hydrolysis of a terminal, unsubstituted xyloside at the extreme reducing end of a xylogluco-oligosaccharide. Representative alpha-xylosidases from glycoside hydrolase family 31 utilize a two-step (double-displacement) mechanism involving a covalent glycosyl-enzyme intermediate, and retain the anomeric configuration of the product.
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
-
the enzyme belongs to the glycoside hydrolase family 31, GH31
physiological function
additional information
-
extensive interactions between the enzyme's active-site variants and xyloglucan hexa- and heptasaccharides, role of the PA14 domain, structure-function analysis using a combination of NMR spectroscopic techniques, including saturation transfer difference and transfer NOE spectroscopy
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-methylumbelliferyl-alpha-D-glucoside + H2O
4-methylumbelliferol + D-glucose
show the reaction diagram
-
-
-
?
4-nitrophenyl alpha-D-glucopyranoside + H2O
4-nitrophenol + alpha-D-glucose
show the reaction diagram
-
low activity
-
-
?
4-nitrophenyl alpha-D-xyloside + H2O
4-nitrophenol + alpha-D-xylose
show the reaction diagram
-
-
-
?
4-nitrophenyl alpha-maltoside + H2O
4-nitrophenyl alpha-D-glucoside + D-glucose
show the reaction diagram
4-nitrophenyl beta-isoprimeveroside + H2O
alpha-D-xylose + 4-nitrophenyl beta-D-glucopyranoside
show the reaction diagram
4-nitrophenyl-alpha-D-glucoside + H2O
4-nitrophenol + alpha-D-glucose
show the reaction diagram
4-nitrophenyl-alpha-D-xylopyranoside + H2O
4-nitrophenol + alpha-D-xylose
show the reaction diagram
-
-
-
?
4-nitrophenyl-alpha-D-xyloside + H2O
4-nitrophenol + alpha-D-xylose
show the reaction diagram
4-nitrophenyl-beta-isoprimeveroside + H2O
4-nitrophenyl-D-glucose + D-xylose
show the reaction diagram
-
-
-
?
alpha-D-Xyl-(1->6)-beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4)-D-Glc + H2O
D-xylose + beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4) D-Glc
show the reaction diagram
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-
-
-
?
alpha-D-xylopyranosyl fluoride + H2O
alpha-D-xylose + fluoride
show the reaction diagram
-
-
-
-
?
isoprimeverose + H2O
alpha-D-xylose + beta-D-glucose
show the reaction diagram
maltose + H2O
D-glucose
show the reaction diagram
maltotetraose + H2O
maltotriose + D-glucose
show the reaction diagram
-
-
-
?
maltotriose + H2O
D-maltose + D-glucose
show the reaction diagram
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc + H2O
?
show the reaction diagram
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-
-
?
xyloglucan + H2O
?
show the reaction diagram
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pea xyloglucan, tamarind xyloglucans, etiolated peas, green peas, corn stover, lamb's quarters
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-
?
xyloglucan + H2O
xylose + ?
show the reaction diagram
xyloglucan oligosaccharide + H2O
?
show the reaction diagram
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extensive interactions between the enzyme's active-site variants and xyloglucan hexa- and heptasaccharides. The enzyme recognizes the entire cello-tetraosyl backbone of the substrate and product in positive enzyme subsites and makes further significant interactions with internal pendant alpha-(1->6)-linked xylosyl units, role of the PA14 domain, stereochemistry of the hydrolysis, overview
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-
?
xyloglucan oligosaccharide + H2O
alpha-D-xylose + ?
show the reaction diagram
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
alpha-D-Xyl-(1->6)-beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4)-D-Glc + H2O
D-xylose + beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4)-[alpha-D-Xyl-(1->6)]-beta-D-Glc-(1->4) D-Glc
show the reaction diagram
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-
-
-
?
additional information
?
-
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the enzyme promotes the release of free glucose and xylose from substrates containing alpha-linked xylose, including isoprimeverose, the heptasaccharide subunit of pea xyloglucan, and tamarind xyloglucan
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
no effect on hydrolysis of 4-nitrophenyl-alpha-D-xyloside: Ca2+, Mg2+, Mn2+, Zn2+, Ni2+, Cu2+, and Co2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(5R)-5-fluoro-alpha-D-xylopyranosyl fluoride
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mechanism-based inactivator
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(5S)-5-fluoro-alpha-D-xylopyranosyl fluoride
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mechanism-based inactivator
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1-deoxynojirimycin
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1-deoxyxylonojirimycin
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D-glucose
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D-xylose
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xyloisofagomine
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.7
4-nitrophenyl-alpha-D-glucopyranoside
-
pH 7.0, 37C
0.39
4-nitrophenyl-alpha-D-xylopyranoside
pH 6, 25C
0.52 - 0.71
4-nitrophenyl-alpha-D-xyloside
0.17 - 0.97
alpha-D-xylopyranosyl fluoride
0.55 - 55
Isoprimeverose
0.7
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc
pH 6, 25C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.046
4-nitrophenyl-alpha-D-glucopyranoside
Escherichia coli
-
pH 7.0, 37C
0.58
4-nitrophenyl-alpha-D-xylopyranoside
Cellvibrio japonicus
B3PBD9
pH 6, 25C
0.13 - 0.173
4-nitrophenyl-alpha-D-xyloside
75 - 195
alpha-D-xylopyranosyl fluoride
2.94 - 51.3
Isoprimeverose
9.39
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc
Cellvibrio japonicus
B3PBD9
pH 6, 25C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0064
4-nitrophenyl-alpha-D-glucopyranoside
Escherichia coli
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pH 7.0, 37C
4620
1.48
4-nitrophenyl-alpha-D-xylopyranoside
Cellvibrio japonicus
B3PBD9
pH 6, 25C
8728
0.18 - 3.33
4-nitrophenyl-alpha-D-xyloside
19529
77.3 - 1220
alpha-D-xylopyranosyl fluoride
19530
0.05 - 93.3
Isoprimeverose
9189
13.4
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc
Cellvibrio japonicus
B3PBD9
pH 6, 25C
41690
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.00045
(5R)-5-fluoro-alpha-D-xylopyranosyl fluoride
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pH 7.0, 37C, mechanism-based inactivator
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0.0098
(5S)-5-fluoro-alpha-D-xylopyranosyl fluoride
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pH 7.0, 37C, mechanism-based inactivator
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0.13
1-deoxynojirimycin
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pH 7.0, 37C
0.0009
1-deoxyxylonojirimycin
-
pH 7.0, 37C
109
D-glucose
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pH 4.8, temperature not specified in the publication
13.7
D-xylose
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pH 4.8, temperature not specified in the publication
0.17
xyloisofagomine
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pH 7.0, 37C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.00126
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isoprimeverose, pH 7.0, 37C, mutant enzyme C307I
0.00545
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isoprimeverose, pH 7.0, 37C, mutant enzyme K414W
0.0187
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4-nitrophenyl-alpha-D-xyloside, pH 7.0, 37C, wild-type enzyme
0.0192
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isoprimeverose, pH 7.0, 37C, mutant enzyme W345I
0.0495
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isoprimeverose, pH 7.0, 37C, mutant enzyme F277Y
0.503
-
pH 7.0, 37C
2.43
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pH 5.5, 75C
20.5
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isoprimeverose, pH 7.0, 37C, wild-type enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.8
-
assay at
6.4
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hydrolysis of 4-nitrophenyl-alpha-D-xyloside
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 8.5
pH 4.5: about 60% of maximal activity, pH 8.5: about 60% of maximal activity
5 - 8
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pH 5.0: about 60% of maximal activity, pH 8.0: about 45% of maximal activity
5 - 9
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pH 5.0: about 35% of maximal activity, pH 9.0: about 65% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50
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hydrolysis of 4-nitrophenyl-alpha-D-xyloside increases up to 50C, activity is rapidly lost at higher temperatures
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.5
calculated from sequence
8.3
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isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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the expression level is lower in the apical part of the inflorescence stem when compared with the basal region
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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a secreted alpha-xylosidase
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Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153)
Bacteroides ovatus (strain ATCC 8483 / DSM 1896 / JCM 5824 / NCTC 11153)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
72000
-
1 * 72000, SDS-PAGE
84432
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1 * 84432, calculated from sequence
84500
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mass spectrometry
88000
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6 * 88000, SDS-PAGE
88079
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6 * 88079, calculated from sequence
89000
-
x * 89000, SDS-PAGE
92000
-
gel filtration
104937
x * 104937, calculated from sequence
113643
x * 113643, calculated from sequence
530000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hexamer
monomer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
crystallographic structures of both the apo enzyme and the trapped covalent 5-fluoro-beta-xylosyl-enzyme intermediate, together with docking studies with the XXXG heptasaccharide the importance of a PA14 domain insert in the recognition of longer oligosaccharides by extension of the active-site pocket
hanging drop method, 2.2 A resolution structure
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.7 - 10.1
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4C, 24 h, stable
716825
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
-
37C, retains full activity for 48 h
35
4 h, 15% loss of activity
45
4 h, 15% loss of activity
47
-
15 min, stable up to
55
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15 min, about 70% loss of activity
90
-
half-life: 38 h
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4C, pH 7.0, retains full activity for several months
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
overexpression in Escherichia coli
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the gene is introduced in a suitable expression vector and used to transform Saccharomyces cerevisiae
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
the expression level of AtXYL1 does not show a clear relationship with growth rates
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D659A
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site-directed mutagenesis, active site mutant, catalytically inactive variant
C307I
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isoprimeverose-hydrolyzing activity of the mutant enzyme is reduced 400fold compared to wild-type enzyme. alpha-Glucosidase activity is not detected
C307I/F308D
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alpha-xylosidase activity of wild-type enzyme is converted into alpha-glucosidase activity. Mutant shows 140fold higher hydrolytic activity against p-nitrophenyl alpha-glucopyranoside than wild-type YicI. The mutant is able to hydrolyze nigerose [alpha-D-Glcp-(1->3)-D-Glcp] and kojibiose [alpha-D-Glcp-(1->2)-D-Glcp], which are not hydrolyzed by the wild-type enzyme. Isoprimeverose-hydrolyzing activity of the L1Chi mutant is decreased by about 3700fold, and that of C307I/F308D is diminished to below the limits of detection. alpha-Glucosidase activity with 4-nitrophenyl alpha-D-glucoside is increased 132fold compared to wild-type activity
F277Y
-
isoprimeverose-hydrolyzing activity of the mutant enzyme is reduced 20fold compared to wild-type enzyme. alpha-Glucosidase activity is not detected (alpha-glucosidase activity of the wild-type enzyme is 96244fold lower than specific activity with isoprimeverose)
K414W
-
isoprimeverose-hydrolyzing activity of the mutant enzyme is reduced 12000fold compared to wild-type enzyme. alpha-Glucosidase activity is not detected
W345I
-
isoprimeverose-hydrolyzing activity of the mutant enzyme is reduced 16000fold compared to wild-type enzyme. alpha-Glucosidase activity is not detected
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
saccharification of cell wall polymers
synthesis
-
utility of enzyme AxlA from Aspergillus niger in supplementation of CTec2/HTec2 from Trichoderma reesei for enhancing release of free Glc and Xyl in combination with commercial enzyme cocktails from dicotyledonous and monocotyledonous plants, overview. AxlA supplementation also improves Glc yields from corn stover treated with the commercial cellulase Accellerase 1000
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