Information on EC 3.2.1.32 - endo-1,3-beta-xylanase

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

EC NUMBER
COMMENTARY hide
3.2.1.32
-
RECOMMENDED NAME
GeneOntology No.
endo-1,3-beta-xylanase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
random endohydrolysis of (1->3)-beta-D-glycosidic linkages in (1->3)-beta-D-xylans
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of O-glycosyl bond
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
(1,3)-beta-D-xylan degradation
-
-
d-xylose degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
3-beta-D-xylan xylanohydrolase
This enzyme is found mostly in marine bacteria, which break down the beta(1,3)-xylan found in the cell wall of some green and red algae. The enzyme produces mainly xylobiose, xylotriose and xylotetraose.
CAS REGISTRY NUMBER
COMMENTARY hide
9025-55-2
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
No. C-59-2
-
-
Manually annotated by BRENDA team
Bacillus sp. (in: Bacteria) No. C-59-2
No. C-59-2
-
-
Manually annotated by BRENDA team
PT-5
-
-
Manually annotated by BRENDA team
PT-5
-
-
Manually annotated by BRENDA team
gene xyl4
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-(3-O-methyl-etab-D-xylopyranosyl)-beta-D-xylopyranoside + H2O
?
show the reaction diagram
-
-
-
?
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-beta-D-xylopyranosyl-beta-D-xylopyranoside + H2O
?
show the reaction diagram
-
-
-
?
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranoside + H2O
beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranose + 4-(trifluoromehtyl)umbelliferone
show the reaction diagram
-
-
-
?
beta-1,3-xylan + H2O
?
show the reaction diagram
beta-1,3-xylan + H2O
beta-1,3-D-xylobiose
show the reaction diagram
beta-1,3-xylan + H2O
beta-1,3-xylobiose + beta-1,3-xylotriose + ?
show the reaction diagram
beta-1,3-xylan + H2O
D-xylose + xylooligosaccharides
show the reaction diagram
-
-
-
?
beta-1,3-xylan + H2O
disaccharides + trisaccharides + tetrasaccharides
show the reaction diagram
-
-
disaccharides, trisaccharides and tetrasaccharides are the major products, whereas the monosaccharides, pentasaccharides and oligosaccharides with more than five xylose units are produces at small quantities
-
?
beta-1,3-xylan + H2O
xylose + xylooligosaccharides
show the reaction diagram
carboxymethylcellulose + H2O
?
show the reaction diagram
-
-
-
-
?
glycol beta-1,3-xylan + H2O
?
show the reaction diagram
glycol-beta-1,3-xylan + H2O
xylose + ?
show the reaction diagram
-
-
-
-
?
laminarin + H2O
?
show the reaction diagram
-
-
-
-
?
rhodymenan + H2O
beta-1,4-xylotriose + beta-1,4-linked xylooligosaccharides
show the reaction diagram
xylan (birchwood) + H2O
xylotetraose + ?
show the reaction diagram
-
-
xylotetraose is main product of xylan degradation
-
?
xylan (larchwood) + H2O
xylotetraose + ?
show the reaction diagram
-
-
xylotetraose is main product of xylan degradation
-
?
xylan (oat spelts) + H2O
xylotetraose + ?
show the reaction diagram
-
-
xylotetraose is main product of xylan degradation
-
?
xylopentaose + H2O
xylose + ?
show the reaction diagram
-
-
-
-
?
xylopentaose + H2O
xylose + xylotetraose + xylobiose + xylotriose
show the reaction diagram
xylotetraose + H2O
xylose + ?
show the reaction diagram
-
-
-
-
?
xylotetraose + H2O
xylose + xylotriose + xylobiose
show the reaction diagram
xylotriose + H2O
xylose + xylobiose
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
beta-1,3-xylan + H2O
?
show the reaction diagram
beta-1,3-xylan + H2O
beta-1,3-xylobiose + beta-1,3-xylotriose + ?
show the reaction diagram
beta-1,3-xylan + H2O
xylose + xylooligosaccharides
show the reaction diagram
D5MP61
-
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
-
activates
Mg2+
-
activates
NaCl
both the enzyme and the binding activities for insoluble beta-1,3-xylan but not soluble glycol-beta-1,3-xylan, are enhanced by NaCl
additional information
Ca2+, Mg2+, and Na+ have no significant effects on enzyme activity
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(3R,4R)-4-hydroxy-3-[beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyloxy]-piperidine
competitive
(3R,4R)-4-hydroxy-3-[beta-D-xylopyranosyloxy]-piperidine
competitive
22,4-dinitrophenyl-beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyl-(1->3)2-deoxy-2-fluoro-beta-D-xylopyranoside
-
dithiothreitol
-
-
Fe2+
complete inhibition at 1 mM
N-bromosuccinimide
Ni2+
45-55% inhibition at 1 mM
Pb(CH3COO)2
-
1 mM, strong
phenyl 1-thio-beta-D-xylopyranoside
-
phenyl 4-O-beta-D-xylopyranosyl-1-thio-beta-D-xylopyranoside
-
phenyl beta-D-xylopyranosyl-(1->3)-1-thio-beta-D-xylopyranoside
-
additional information
dithiothreitol, and EDTA have no significant effects on enzyme activity
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
dithiothreitol
-
activates
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
71
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-(3-O-methyl-etab-D-xylopyranosyl)-beta-D-xylopyranoside
at pH 7.5 and 37°C
1.7
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-beta-D-xylopyranosyl-beta-D-xylopyranoside
at pH 7.5 and 37°C
0.0038
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranoside
at pH 7.5 and 37°C
0.75
xylopentaose
-
pH 7.5, 37°C
0.74
xylotetraose
-
pH 7.5, 37°C
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.1
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-(3-O-methyl-etab-D-xylopyranosyl)-beta-D-xylopyranoside
at pH 7.5 and 37°C
1.9
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-beta-D-xylopyranosyl-beta-D-xylopyranoside
at pH 7.5 and 37°C
0.89
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranoside
at pH 7.5 and 37°C
588.2
beta-1,3-xylan
at pH 6.5 and 85°C
322.6
glycol beta-1,3-xylan
at pH 6.5 and 85°C
14000
xylopentaose
-
pH 7.5, 37°C
350
xylotetraose
-
pH 7.5, 37°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-(3-O-methyl-etab-D-xylopyranosyl)-beta-D-xylopyranoside
at pH 7.5 and 37°C
1.1
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl 3-O-beta-D-xylopyranosyl-beta-D-xylopyranoside
at pH 7.5 and 37°C
230
2-oxo-4-(trifluoromethyl)-2H-chromen-7-yl beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranoside
at pH 7.5 and 37°C
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.002
(3R,4R)-4-hydroxy-3-[beta-D-xylopyranosyl-(1->3)-beta-D-xylopyranosyloxy]-piperidine
at pH 7.5 and 37°C
0.0031
(3R,4R)-4-hydroxy-3-[beta-D-xylopyranosyloxy]-piperidine
at pH 7.5 and 37°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.7
-
-
6.4
-
enzyme form EF-3 and EF-5
8.5
-
enzyme form EF-4
9.3
-
enzyme form EF-2
9.9
-
-
13.3
-
enzyme form EF-6
13.6
-
-
15.2
-
enzyme form EF-1
207
-
xylan (oat spelts), pH 6.0, 30°C
225
-
xylan (birchwood), pH 6.0, 30°C
226
-
laminarin, pH 6.0, 30°C
253
-
xylan (larchwood), pH 6.0, 30°C
additional information
-
-
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4
-
enzyme form EF-4
4.5
-
enzyme forms EF-5 and EF-6
5
-
enzyme forms EF-1 and EF-3
5.5
-
enzyme form EF-2
6 - 6.5
-
-
6 - 7.5
-
-
7 - 7.5
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4 - 10
-
about 50% of maximal activity at pH 4.0 and at pH 10.0
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
-
enzyme form EF-2
50
-
enzyme form EF-3 and EF-6
55
-
enzyme form EF-1
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 70
-
about 20% of maximal activity at 30°C and at 70°C
37 - 60
-
37°C: optimum, 60°C: does not hydrolyze beta-1,3-xylan above 60°C at pH 7.5
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.6 - 4.7
-
or higher, enzyme Xyl I
5
calculated from amino acid sequence
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
UNIPROT
ORGANISM
Vibrio sp;
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20000
-
x * 20000, SDS-PAGE, x * 20000-24000, gel filtration
35000
-
1 * 35000, SDS-PAGE
36000
-
gel filtration
38000
x * 38000, SDS-PAGE
38033
x * 38033, calculated from amino acid sequence
49264
x * 49264, calculated
52000
-
x * 52000, SDS-PAGE
53000
-
gel filtration
59000
-
x * 59000, SDS-PAGE
63000
x * 63000, SDS-PAGE
340000
-
PAGE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
monomer
multimer
-
x * 20000, SDS-PAGE, x * 20000-24000, gel filtration
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
structure of recombinant carbohydrate-binding module of beta-1,3-xylanase is determined at a resolution of 1.25 A
-
to 1.8 A resolution, space group P21
-
sitting-drop and hanging-drop vapour-diffusion method, crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 51.6 A, b = 75.8 A, c = 82.0 A. X-ray diffraction data are collected to 1.44 A resolution
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
3 - 6
-
30°C, 1 h, stable
136244
3 - 10
the enzyme remains stable at pH 3.0-10.0 after incubation at 4°C for 20 h
729069
4
-
4°C, 24 h, 35% loss of activity
136250
4.5 - 10
-
4°C, 20 h, stable
136243
5 - 9
-
50°C, 10 min, stable
136246
5 - 8
-
4°C, 20 h, stable
136251
5.5 - 8
-
4°C, 20 h, stable
136249
6 - 10
-
4°C, 24 h, enzyme retains 90-100% of activity
136250
7 - 7.5
-
60°C, 10 min, stable
136246
8
-
30°C, 1 h, almost all activity is lost
136244
12
-
4°C, 24 h, retains 70% of its activity
136250
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
stable below
55
-
pH 6.0, 15 min, complete loss of activity
80 - 85
the enzyme activity half-life is 23.9 h at 85°C and retains over 80% of initial activity at 80°C for 24 h
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
0°C, stable for more than 3 months
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
6 different enzyme forms: EF-1, EF-2, EF-3, EF-4, EF-5 and EF-6
-
HisTrap HP column chromatography and HiTrap Q column chromatography
nickel affinity column chromatography and Superdex 200 gel filtration
recombinant
-
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL2(DE3) by nickel affinity and beta-1,3-xylan affinity chromatography and gel filtration
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed as a fusion protein with tandem repeats of the N-terminal domain of Protein S from Myxocuccus xanthus in Escherichia coli BL21(DE3) cells. ArgHCl efficiently solubilizes the fusion protein
expressed in Escherichia coli
expressed in Escherichia coli BL21(DE3) cells
expressed in Escherichia coli BL21(DELTADE3)pLysS cells
-
expression in Escherichia coli
expression in Escherichia coli DH5alpha
-
gene xyl4, DNA and amino acid sequence determination and comparison, expression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
wild-type and mutant enzymes are expressed in Escherichia coli
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E126Q/E238Q
inactive
E126Q
-
inactive
-
E126Q/E238Q
-
inactive
-
E238Q
-
inactive
-
E138D
-
activity is extremely low
E138Q
-
inactive mutant
E234D
-
activity is extremely low
E234Q
-
inactive mutant
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis