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Information on EC 3.2.1.37 - xylan 1,4-beta-xylosidase and Organism(s) Geobacillus stearothermophilus and UniProt Accession Q9ZFM2

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IUBMB Comments
Also hydrolyses xylobiose. Some other exoglycosidase activities have been found associated with this enzyme in sheep liver.
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This record set is specific for:
Geobacillus stearothermophilus
UNIPROT: Q9ZFM2
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The taxonomic range for the selected organisms is: Geobacillus stearothermophilus
The expected taxonomic range for this enzyme is: Eukaryota, Bacteria, Archaea
Synonyms
beta-xylosidase, alpha-l-arabinofuranosidase, xylosidase, beta-d-xylosidase, xyl i, xynb2, xyl3a, xln-dt, xynb3, xyl43a, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1,4-beta-D-xylan xylohydrolase
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beta-D-xylopyranosidase
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beta-D-xylosidase
beta-xylosidase
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exo-1,4-beta-D-xylosidase
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exo-1,4-beta-xylosidase
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Exo-beta-(1,4)-xylanase
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Xylan 1,4-beta-xylosidase
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xylobiase
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additional information
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of O-glycosyl bond
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PATHWAY SOURCE
PATHWAYS
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SYSTEMATIC NAME
IUBMB Comments
4-beta-D-xylan xylohydrolase
Also hydrolyses xylobiose. Some other exoglycosidase activities have been found associated with this enzyme in sheep liver.
CAS REGISTRY NUMBER
COMMENTARY hide
9025-53-0
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SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2,5-dinitrophenyl-beta-D-xylopyranoside + H2O
2,5-dinitrophenol + beta-D-xylose
show the reaction diagram
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?
2,5-dinitrophenyl-beta-D-xylopyranoside + H2O
2,5-dinitrophenol + D-xylopyranose
show the reaction diagram
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?
2-nitrophenyl beta-D-xylopyranoside + H2O
2-nitrophenol + beta-D-xylopyranose
show the reaction diagram
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-
?
3,4-dinitrophenyl beta-D-xylopyranoside + H2O
3,4-dinitrophenol + beta-D-xylopyranose
show the reaction diagram
3,5-dinitrophenyl beta-D-xylopyranoside + H2O
3,5-dinitrophenol + beta-D-xylose
show the reaction diagram
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-
-
?
4-bromophenyl-beta-D-xylopyranoside + H2O
4-bromophenol + beta-D-xylose
show the reaction diagram
low activity of mutant E178G, no activity of the wild-type enzyme
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?
4-methylumbelliferyl-beta-D-xylopyranoside + H2O
4-methylumbelliferol + beta-D-xylose
show the reaction diagram
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?
4-nitrophenyl beta-D-xylopyranoside + H2O
4-nitrophenol + beta-D-xylopyranose
show the reaction diagram
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?
4-nitrophenyl beta-D-xylopyranoside + H2O
4-nitrophenol + beta-D-xylose
show the reaction diagram
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?
p-nitrophenyl beta-D-xyloside + H2O
p-nitrophenol + beta-D-xylose
show the reaction diagram
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?
xylan + H2O
beta-D-xylose + ?
show the reaction diagram
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complete degration of xylan requires synergistic action of two types of enzyme, endo-1,4-xylanase to form xylooligosaccharides and beta-D-xylosidase, which hydrolyses xylooligosaccharides to xylose
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?
xylo-oligosaccharides + H2O
beta-D-xylose + ?
show the reaction diagram
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derived from xylan
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?
xylobiose + H2O
2 beta-D-xylose
show the reaction diagram
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?
additional information
?
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substrate specificity of wild-type enzyme and mutant E178G, the mutant enzyme shows residual activity with 2-naphthyl-beta-D-xylopyranoside, 3,4-dimethylphenyl-beta-D-xylopyranoside, and 3-nitrophenyl-beta-D-xylopyranoside, while the wild-type enzyme is inactive with these substrates, overview
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?
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
xylan + H2O
beta-D-xylose + ?
show the reaction diagram
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complete degration of xylan requires synergistic action of two types of enzyme, endo-1,4-xylanase to form xylooligosaccharides and beta-D-xylosidase, which hydrolyses xylooligosaccharides to xylose
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?
xylo-oligosaccharides + H2O
beta-D-xylose + ?
show the reaction diagram
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derived from xylan
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?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
the enzyme is not affected by 1 mM of Fe3+, Ca2+, Co2+, Mg2+, Ba2+, Ni2+, K+, Zn2+, Cu2+, or EDTA
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ag+
97% inhibition at 1 mM
Hg2+
complete inhibition at 1 mM, 93% inhibition at 0.1 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.016 - 0.95
2,5-dinitrophenyl-beta-D-xylopyranoside
0.18 - 7.1
2-nitrophenyl-beta-D-xylopyranoside
0.025 - 0.8
3,4-dinitrophenyl-beta-D-xylopyranoside
0.27 - 5.2
4-nitrophenyl-beta-D-xylopyranoside
1.2
p-nitrophenyl beta-D-xyloside
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additional information
additional information
steady-state kinetics, recombinant wild-type and mutant enzymes
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
25 - 30
2,5-dinitrophenyl-beta-D-xylopyranoside
1.8 - 77
3,4-dinitrophenyl-beta-D-xylopyranoside
20
4-methylumbelliferyl-beta-D-xylopyranoside
pH 7.0, 40°C, recombinant wild-type enzyme
0.014 - 57
4-nitrophenyl-beta-D-xylopyranoside
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
pH profiles, wild-type and mutant enzymes, overview
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
temperature profile and thermal stability
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
XYNB_GEOSE
504
0
58119
Swiss-Prot
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
58000
4 * 58000, deduced from gene sequence, crystallization data
150000
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gel filtration, SDS-PAGE
75000
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2 * 75000, SDS-PAGE
79894
2 * 79894, sequence calculation and crystal structure
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
4 * 58000, deduced from gene sequence, crystallization data
dimer
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
native enzyme and selenomethionyl derivative
in complex with substrate xylobiose. The xylose moiety at the K1 subsite is held by a large number of hydrogen bonds, whereas only one hydroxyl of the xylose unit at the C1 subsite can create hydrogen bonds with the enzyme. The general base, Asp15, is located on the alpha-side of the K1 xylose sugar ring, 5.2 A from the anomeric carbon. This location enables it to activate a water molecule for a single displacement attack on the anomeric carbon, resulting in inversion of the anomeric configuration. Glu187, the general acid, is 2.4 A from the glycosidic oxygen atom and can protonate the leaving aglycon. The third catalytic carboxylic acid, Asp128, is 4 A from the general acid, modulating its pKa and keeping it in the correct orientation relative to the substrate
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purified recombinant enzyme, hanging drop vapour diffusion method, 0.002 ml protein solution containing 5 mg/ml protein in 50 mM Tris-HCl, pH 7.0, 100 mM NaCl, and 0.02% NaN3, is mixed with 0.002 ml well solution containing 2.3-2.4 M ammonium sulfate, and 40-60 mM sodium citrate at pH 5.5, a few weeks, X-ray diffraction structure determination and analysis at 2.0 A resolution
purified recombinant wild-type and mutant D15G, D128G, and E178G XynB3s, 22-30 mg/ml protein, 0.005 ml protein solution is mixed with 0.005 ml reservoir solution and 0.001 ml detergent solution, equilibration to 0.5 ml with reservoir solution, X-ray diffraction structure determination and preliminary analysis at 2.2-2.5 A resolution
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D128G
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme, nearly inactive mutant
D15G
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme, nearly inactive mutant
E160A
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E160 is the acid-base catalyst
E178G
site-directed mutagenesis, the mutant shows an altered substrate specificity and highly reduced activity compared to the wild-type enzyme
E335G
nucleophile-deficient mutant enzyme can function as an efficient glycosynthase, using alpha-D-xylopyranosyl fluoride as a donor and various aryl sugars as acceptors. The mutant enzyme can also catalyze the self-condensation reaction of alpha-D-xylopyranosyl fluoride, providing mainly alpha-D-xylobiosyl fluoride
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
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stable within
136288
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
temperature profile and thermal stability
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli strain BL21(DE3) to near homogeneity
recombinant enzyme, expressed in Escherichia coli
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recombinant soluble wild-type and mutant D15G, D128G, and E178G enzymes from Escherichia coli strain BL21(DE3) by heat treatment and gel filtration
recombinant soluble wild-type, 2.6fold to over 95% purity, and mutant enzymes from Escherichia coli strain BL21(DE3) by heat treatment and gel filtration
to homogeneity by 4step chromatography
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CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene xynB2, overexpression of the soluble enzyme in Escherichia coli strain BL21(DE3)
gene xynB3, expression of soluble wild-type and mutant D15G, D128G, and E178G enzymes in Escherichia coli strain BL21(DE3)
gene xynB3, expression of soluble wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
synthesis
formation of xylooligosaccharides from alpha-D-xylopyranosyl fluoride in a conjugated reaction between beta-xylosidase E335G mutant enzyme and endo-1,4-beta-xylanase E265G mutant enzyme
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Nanmori, T.; Watanabe, T.; Shinke, R.; Kohno, A.; Kawamura, Y.
Purification and properties of thermostable xylanase and beta-xylosidase produced by a newly isolated Bacillus stearothermophilus strain
J. Bacteriol.
172
6669-6672
1990
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Czjzek, M.; Bravman, T.; Henrissat, B.; Shoham, Y.
Crystallization and preliminary x-ray analysis of family 39 beta-D-xylosidase from Geobacillus stearothermophilus T-6
Acta Crystallogr. Sect. D
D60
583-585
2004
Geobacillus stearothermophilus (Q9ZFM2), Geobacillus stearothermophilus T-6 (Q9ZFM2)
Manually annotated by BRENDA team
Bravman, T.; Mechaly, A.; Shulami, S.; Belakhov, V.; Baasov, T.; Shoham, G.; Shoham, Y.
Glutamic acid 160 is the acid-base catalyst of beta-xylosidase from Bacillus stearothermophilus T-6: a family 39 glycoside hydrolase
FEBS Lett.
495
115-119
2001
Geobacillus stearothermophilus, Geobacillus stearothermophilus T-6
Manually annotated by BRENDA team
Czjzek, M.; Bravman, T.; Henrissat, B.; Shoham, Y.
Crystallization and preliminary crystallographic analysis of a thermostable family 52 beta-D-xylosidase from Geobacillus stearothermophilus T-6
Acta Crystallogr. Sect. D
D60
1461-1463
2004
Geobacillus stearothermophilus (Q09LZ0)
Manually annotated by BRENDA team
Bruex, C.; Niefind, K.; Ben-David, A.; Leon, M.; Shoham, G.; Shoham, Y.; Schomburg, D.
Crystallization and preliminary crystallographic analysis of a family 43 beta-D-xylosidase from Geobacillus stearothermophilus T-6
Acta Crystallogr. Sect. F
F61
1054-1057
2005
Geobacillus stearothermophilus (Q09LX0)
Manually annotated by BRENDA team
Shallom, D.; Leon, M.; Bravman, T.; Ben-David, A.; Zaide, G.; Belakhov, V.; Shoham, G.; Schomburg, D.; Baasov, T.; Shoham, Y.
Biochemical characterization and identification of the catalytic residues of a family 43 beta-D-xylosidase from Geobacillus stearothermophilus T-6
Biochemistry
44
387-397
2005
Geobacillus stearothermophilus (Q09LX0)
Manually annotated by BRENDA team
Bruex, C.; Ben-David, A.; Shallom-Shezifi, D.; Leon, M.; Niefind, K.; Shoham, G.; Shoham, Y.; Schomburg, D.
The structure of an inverting GH43 beta-xylosidase from Geobacillus stearothermophilus with its substrate reveals the role of the three catalytic residues
J. Mol. Biol.
359
97-109
2006
Geobacillus stearothermophilus
Manually annotated by BRENDA team
Ben-David, A.; Bravman, T.; Balazs, Y.S.; Czjzek, M.; Schomburg, D.; Shoham, G.; Shoham, Y.
Glycosynthase activity of Geobacillus stearothermophilus GH52 beta-xylosidase: efficient synthesis of xylooligosaccharides from alpha-D-xylopyranosyl fluoride through a conjugated reaction
Chembiochem
8
2145-2151
2007
Geobacillus stearothermophilus (Q09LZ0), Geobacillus stearothermophilus, Geobacillus stearothermophilus T-6 (Q09LZ0)
Manually annotated by BRENDA team