Information on EC 3.2.1.136 - glucuronoarabinoxylan endo-1,4-beta-xylanase

Word Map on EC 3.2.1.136
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
Specify your search results
Select one or more organisms in this record:
Show additional data
Do not include text mining results
Include (text mining) results (more...)
Include results (AMENDA + additional results, but less precise; more...)


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

EC NUMBER
COMMENTARY hide
3.2.1.136
-
RECOMMENDED NAME
GeneOntology No.
glucuronoarabinoxylan endo-1,4-beta-xylanase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Endohydrolysis of (1->4)-beta-D-xylosyl links in some glucuronoarabinoxylans
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis
hydrolysis of O-glycosyl bond
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
glucuronoarabinoxylan degradation
-
-
SYSTEMATIC NAME
IUBMB Comments
glucuronoarabinoxylan 4-beta-D-xylanohydrolase
High activity towards feruloylated arabinoxylans from cereal plant cell walls.
CAS REGISTRY NUMBER
COMMENTARY hide
123609-77-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
beta-xylanase M4
-
-
Manually annotated by BRENDA team
fragment of 387 bp, part of the gene cxo; CDBB-531
UniProt
Manually annotated by BRENDA team
fragment of 387 bp, part of the gene cxo; CDBB-531
UniProt
Manually annotated by BRENDA team
beta-xylanase M2
-
-
Manually annotated by BRENDA team
varieties Legat and Astuce, additionally microbial washed off activity of endoxylanase is investigated
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
glucuronoxylanase Xyn30D is a modular enzyme containing a family 30 glycoside hydrolase catalytic domain and an attached carbohydrate binding module of the CBM35 family. GH30 family enzymes structure comparisons, overview
metabolism
the enzyme plays a role in depolymerization of highly substituted chemically complex xylans, it belongs to the secretome of Paenibacillus barcinonensis, a powerful xylan degrading microorganism that shows a complex set of carbohydratases, including several GH10 and GH11 xylanases
additional information
the catalytic domain folds into an (alpha/beta)8 barrel with an associated beta-structure, whereas the attached CBM35 domain displays a jellyroll beta-sandwich including two calcium ions, molecular surface of Xyn30D-CBM35, atomic interactions between Xyn30D-CBM35, the calcium ion and the GlcA ligand, overview. An extended 12-residue segment links the CBM35 to the catalytic GH30 domain. Although both domains fold in an independent manner, the linker region makes polar interactions with the catalytic domain, allowing a moderate flexibility
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-O-methyl-alpha-D-glucuronosyl-(1->2)-beta-D-xylopyranosyl-(1->4)-beta-D-xylopyranosyl-(1->4)-D-xylose + H2O
?
show the reaction diagram
-
-
-
?
4-O-methyl-beta-D-glucuronopyranosyl-1,2-(beta-1,4-xylan) + H2O
4-O-methyl-beta-D-glucopyranuronosyl-(1-2)-[beta-D-xylopyranosyl-(1-4)]-beta-D-xylopyranosyl-(1-4)-beta-D-xylopyranosyl-(1-4)-beta-D-xylopyranose + ?
show the reaction diagram
-
-
-
-
?
4-O-methyl-D-glucoxylan + H2O
?
show the reaction diagram
-
elimination of the carboxyl groups of substrate leads to more than 300fold reduction of specific activity
-
-
?
4-O-methyl-D-glucuronoxylan + H2O
?
show the reaction diagram
-
esterification of substrate leads to more than 300fold reduction of specific activity
-
-
?
4-O-methyl-D-glucuronoxylan methyl ester + H2O
?
show the reaction diagram
-
-
-
-
?
4-O-methylglucuronoxylan + H2O
?
show the reaction diagram
arabinoxylan + H2O
reduced sugars
show the reaction diagram
-
azurine-cross-linked arabinoxylan
-
-
?
arabinoxylan + H2O
reducing sugars
show the reaction diagram
beechwood xylan + H2O
?
show the reaction diagram
beta-D-xylopyranosyl-(1->4)-[4-O-methyl-alpha-D-glucuronosyl-(1->2)]-beta-D-xylopyranosyl-(1->4)-beta-D-xylopyranosyl-(1->4)-D-xylose + h2O
?
show the reaction diagram
-
-
-
?
birchwood xylan + H2O
?
show the reaction diagram
-
-
-
?
feraxan + H2O
?
show the reaction diagram
glucuronoarabinoxylan + H2O
reduced xylose + ?
show the reaction diagram
-
-
-
-
?
glucuronoarabinoxylan-lignin + H2O
reduced xylose + ?
show the reaction diagram
-
four types of in vitro reconstituted non-covalent glucuronoarabinoxylan-model lignin nanocomposites, each displaying different lignin contents, are synthesized as enzyme substrates, method overview. The nanocomposites contain a mixture of free glucuronoarabinoxylan chains with non-covalent glucuronoarabinoxylan-lignin complexes, morphology and size distribution analysis. Increased particle size is directly related to the solubility and reactivity of coniferyl alcohol, as reflected by changes in the amount of beta-O-4 linkages. Negative correlation between the proportion and organization patterns of lignin dehydrogenation polymer in the nanocomposites and enzyme activity, kinetic analysis
-
-
?
glucuronoxylan + H2O
?
show the reaction diagram
the cleavage of the glucuronoxylan main chain takes place exclusively at the second glycosidic linkage from the branch towards the reducing end of the polysaccharide chain
-
-
?
lignocellulose + H2O
reducing sugars
show the reaction diagram
maize xylan + H2O
?
show the reaction diagram
-
i.e. heteroxylan with glucuronic acid side chain, enzyme recognizes glucuronic acid side chains along the xylan main chain and mediates hydrolysis of beta-1,4-xylosyl linkages of adjacent unsubstituted xylosyl residues, endo-type hydrolase, possible recognition sites
-
-
?
oat spelt xylan + H2O
?
show the reaction diagram
Remazol brilliant blue-carboxymethylcellulose + H2O
glucose + cellobiose + cellotriose + cellotetraose + high-molecular-mass oligosaccharides
show the reaction diagram
-
cellulose activity
-
?
rye arabinoxylan + H2O
?
show the reaction diagram
-
-
-
?
rye glucuronoarabinoxylan + H2O
?
show the reaction diagram
the enzyme shows calcium-dependent glucuronic acid binding and also some binding to arabinose in presence of calcium chelating EDTA. Recognition of uronic acid by the CBM35 domains is always dependent on calcium, which interacts with the carboxylate of the ligand. Glu129, from the loop linking beta10-beta11, is a determinant of substrate specificity
-
-
?
Vigna angularis xylan + H2O
?
show the reaction diagram
-
i.e. heteroxylan with glucuronic acid side chain
-
-
?
wheat arabinoxylan + H2O
?
show the reaction diagram
xylan + H2O
xylose + arabinose + xylobiose + high-molecular-mass oligosaccharides
show the reaction diagram
xylan from birchwood
xylanase activity
-
?
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
additional information
?
-
-
the enzyme recognizes glucuronic acid side chains along the xylan main chain and mediates the hydrolysis of the beta-1,4-xylosyl linkages of the adjacent unsubstituted xylosyl residues
-
-
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
partial inhibition
additional information
-
wheat kernels contain endogenous endoxylanase inhibitors that interfere with enzyme activity and differ between the wheat varieties
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
additional information
cellulose
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.14
-
substrate 4-O-methyl-D-glucuronoxylan methyl ester, pH 5.5, 35C
0.15
-
substrate 4-O-methyl-D-glucoxylan, pH 5.5, 35C
9.5
-
substrate wheat arabinoxylan , pH 6.0, 70C
46
-
substrate 4-O-methyl-D-glucuronoxylan, pH 5.5, 35C
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7
highest cellulase activity in phosphate buffer, about 10% less activity than in citrate-phosphate buffer; highest xylanase activity in citrate-phosphate buffer, 10% less activity than in Tris-HCl
9
highest xylanase activity in Tris-HCl buffer
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 10
pH 5-7: sodium citrate-phosphate buffer, pH 5-8: phosphate buffer, pH 7-10: Tris-HCl buffer
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35
-
assay at
37
-
assay at
50
for cellulase and xylanase activity
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.3
isoelectric focusing in 5% polyacrylamide gel, pH 3.5-10 Ampholine, 200 V, 50 min, bands visualized with Coomassie brilliant blue G250 or silver staining, standard proteins of pI 3.5-9.3
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
Xyn30D is a modular enzyme
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
purified recombinant His-tagged XynC, 5 mg/ml protein in 20 mM HEPES, 150 mM NaCl pH 7.2, is mixed with 0.2 M sodium tartrate and 20% PEG 3350, which results in a crystal-positive condition with 0.1 M sodium malonate pH 7.0, X-ray diffraction structure determination and analysis at 1.64-2.7 A resolution, molecular replacement
in complex with 4-O-methylaldotetrauronic acid or glucuronate, hanging drop vapor diffusion method, using 200 mM sodium tartrate and 200 mM sodium malonate (pH 7.0) in 19% (w/v) polyethylene glycol 3350
in complex with beta-D-xylopyranosyl-(1->4)-[4-O-methyl-alpha-D-glucuronosyl-(1->2)]-beta-D-xylopyranosyl-(1->4)-D-xylose,hanging drop vapor diffusion method, using 0.1 M imidazole/D,L-malic acid buffer (pH 7.5) and 20% (w/v) poly(ethylene glycol) 1500
-
purified recombinant catalytic domain GH30 or extended domain CBM35, free or in complex with glucuronic acid, crystallization by mixing of 0.001 ml of 22 mg/ml protein in 20 mM Tris, pH 8.0, and 150 mM NaCl with 0.001 ml of a solution containing 20% w/v PEG 6000, 0.2 M Ca2Cl, and either 0.1 M MES, pH 6.0, or 0.1 M Hepes, pH 7.0, and equilibration by vapor diffusion at room temperature, complexes are obtained by the soaking technique using glucuronic acid or a mixture of aldotriouronic, aldotetraouronic, and aldopentaouronic acids, in a ratio of 2:2:1, cryoprotection by 20% v/v glycerol, X-ray diffraction structure determination and analysis at 2.4 A resolution, molecular replacement, modelling
modeling of strucuture. The protein displays a jelly roll beta-sandwich fold presenting two potential carbohydrate binding clefts, A and B. The cleft A, is located between two loops connecting b4-b5 and b8-b9 strands. Tyr28 and Phe84 present on these loops make a planar hydrophobic binding surface to accommodate sugar ring of ligand. The cleft B, is located on concave surface of beta-sandwich fold. Tyr34 and Tyr104 make a planar hydrophobic platform, which may be inaccessible to ligand due to hindrance by Pro68
-
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 9
-
60C, enzyme is completely stable
646829
5.5 - 9
-
85C, enzyme shows about 50% of its original activity
646829
10
-
55C, enzyme is completely stable
646829
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
at pH 10.0, enzyme is completely stable
60
-
between pH 5.0-9.0, enzyme is completely stable
82
-
melting temperature
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
activity preserved after 7 weeks in incubation chamber
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
Freeze drying and concentration of washing liquid from kernels does not change endoxylanase activity.
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
centrifuged supernatant concentrated with membrane filter, applied to Bio-Gel P100 gel filtration column, cellulolytic fractions pooled, lyophilized, dissolved, loaded onto hydroxylapatite column, last steps repeated, 4 degrees Celsius, purity monitored by SDS-PAGE and isoelectric focusing
MEP HyperCel column chromatography, SP Sepharose column chromatography, and XK 26/20 column chromatography
-
recombinant His-tagged full-length enzyme and isolated catalytic domain from Escherichia coli strain BL21Star (DE3) by immobilized metal affinity chromatography
recombinant His-tagged XynC from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
shaking of wheat kernels with acetate buffer (25 mM, pH 5.0, 0.02% sodium azide) for 17 h, liquid phase dialyzed against 10 mM sodium acetate buffer, pH 5.0 at 7 degrees Celsius for 24 h, dialysate concentrated by freeze-drying and resuspension in water
-
to near homogeneity
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Escherichia coli DH5alpha as transforming host, Escherichia coli XLI-Blue MRA (P2), cloning vector pBluescript SKII, 37 degrees Celsius, Luria-Bertoni broth
expressed in Bacillus subtilis strain A164delta5
-
expression of His-tagged full-length enzyme and isolated catalytic domain in Escherichia coli strain BL21Star (DE3)
gene ynfF, expression of His-tagged XynC in Escherichia coli strain BL21(DE3)
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
F84A
-
mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans
Y28A
-
mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans
Y28A/F28A
-
mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans
F84A
-
mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans
-
Y28A
-
mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans
-
Y28A/F28A
-
mutant has completely lost its binding affinity towards both glucuronic acid as well as arabinose substituted xylans
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biofuel production
food industry
-
endogenous endoxylanase activity during fermentation and storing can have negative effects on dough, the enzyme effect depends on the wheat variety's enzyme content and inhibitor content