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Information on EC 3.2.1.177 - alpha-D-xyloside xylohydrolase and Organism(s) Cellvibrio japonicus and UniProt Accession B3PBD9

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IUBMB Comments
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.
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Cellvibrio japonicus
UNIPROT: B3PBD9
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The taxonomic range for the selected organisms is: Cellvibrio japonicus
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Reaction Schemes
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Hydrolysis of terminal, non-reducing alpha-D-xylose residues with release of alpha-D-xylose.
Synonyms
alpha-xylosidase, atxyl1, mexyl31, cjxyl31a, xyl31a, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
alpha-xylosidase
alpha-xylosidase 31A
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PATHWAY SOURCE
PATHWAYS
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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.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
4-nitrophenyl-alpha-D-xylopyranoside + H2O
4-nitrophenol + alpha-D-xylose
show the reaction diagram
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-
?
isoprimeverose + H2O
alpha-D-xylose + beta-D-glucose
show the reaction diagram
kcat/KM is 11.5% compared to the value for 4-nitrophenyl-beta-isoprimeveroside
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Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc + H2O
?
show the reaction diagram
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?
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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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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additional information
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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
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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?
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.39
4-nitrophenyl-alpha-D-xylopyranoside
pH 6, 25°C
55
Isoprimeverose
pH 6, 25°C
0.7
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc
pH 6, 25°C
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.58
4-nitrophenyl-alpha-D-xylopyranoside
pH 6, 25°C
2.94
Isoprimeverose
pH 6, 25°C
9.39
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc
pH 6, 25°C
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1.48
4-nitrophenyl-alpha-D-xylopyranoside
pH 6, 25°C
0.05
Isoprimeverose
pH 6, 25°C
13.4
Xyl-alpha-(1->6)-Glc-beta-(1->4)-Glc
pH 6, 25°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
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
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
the enzyme is involved in xyloglucan saccharification
evolution
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the enzyme belongs to the glycoside hydrolase family 31, GH31
additional information
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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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
113643
x * 113643, calculated from sequence
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 113643, calculated from sequence
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
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D659A
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site-directed mutagenesis, active site mutant, catalytically inactive variant
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35
4 h, 15% loss of activity
45
4 h, 15% loss of activity
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression in Escherichia coli
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
biotechnology
saccharification of cell wall polymers
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Larsbrink, J.; Izumi, A.; Ibatullin, F.; Nakhai, A.; Gilbert, H.J.; Davies, G.J.; Brumer, H.
Structural and enzymatic characterisation of a glycoside hydrolase family 31 alpha-xylosidase from Cellvibrio japonicus involved in xyloglucan saccharification
Biochem. J.
436
567-580
2011
Cellvibrio japonicus (B3PBD9), Cellvibrio japonicus
Manually annotated by BRENDA team
Silipo, A.; Larsbrink, J.; Marchetti, R.; Lanzetta, R.; Brumer, H.; Molinaro, A.
NMR spectroscopic analysis reveals extensive binding interactions of complex xyloglucan oligosaccharides with the Cellvibrio japonicus glycoside hydrolase family 31 alpha-xylosidase
Chemistry
18
13395-13404
2012
Cellvibrio japonicus
Manually annotated by BRENDA team