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PDBsum entry 3c7g
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Contents |
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* Residue conservation analysis
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PDB id:
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Hydrolase
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Title:
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Crystal structure of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase from bacillus subtilis in complex with xylotetraose.
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Structure:
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Endo-1,4-beta-xylanase. Chain: a. Synonym: xylanase d. Engineered: yes
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Source:
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Bacillus subtilis. Organism_taxid: 1423. Gene: xynd. Expressed in: escherichia coli. Expression_system_taxid: 562
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Resolution:
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2.02Å
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R-factor:
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0.145
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R-free:
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0.187
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Authors:
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E.Vandermarliere,T.M.Bourgois,M.D.Winn,S.Van Campenhout,G.Volckaert, S.V.Strelkov,J.A.Delcour,A.Rabijns,C.M.Courtin
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Key ref:
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E.Vandermarliere
et al.
(2009).
Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family.
Biochem J,
418,
39-47.
PubMed id:
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Date:
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07-Feb-08
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Release date:
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18-Nov-08
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PROCHECK
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Headers
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References
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Q45071
(XYND_BACSU) -
Arabinoxylan arabinofuranohydrolase from Bacillus subtilis (strain 168)
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Seq:
Struc:
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513 a.a.
488 a.a.*
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Key: |
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PfamA domain |
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Secondary structure |
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CATH domain |
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*
PDB and UniProt seqs differ
at 1 residue position (black
cross)
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Enzyme class:
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E.C.3.2.1.55
- non-reducing end alpha-L-arabinofuranosidase.
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Reaction:
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Hydrolysis of terminal non-reducing alpha-L-arabinofuranoside residues in alpha-L-arabinosides.
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Biochem J
418:39-47
(2009)
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PubMed id:
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Structural analysis of a glycoside hydrolase family 43 arabinoxylan arabinofuranohydrolase in complex with xylotetraose reveals a different binding mechanism compared with other members of the same family.
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E.Vandermarliere,
T.M.Bourgois,
M.D.Winn,
S.van Campenhout,
G.Volckaert,
J.A.Delcour,
S.V.Strelkov,
A.Rabijns,
C.M.Courtin.
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ABSTRACT
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AXHs (arabinoxylan arabinofuranohydrolases) are alpha-L-arabinofuranosidases
that specifically hydrolyse the glycosidic bond between arabinofuranosyl
substituents and xylopyranosyl backbone residues of arabinoxylan. Bacillus
subtilis was recently shown to produce an AXH that cleaves arabinose units from
O-2- or O-3-mono-substituted xylose residues: BsAXH-m2,3 (B. subtilis AXH-m2,3).
Crystallographic analysis reveals a two-domain structure for this enzyme: a
catalytic domain displaying a five-bladed beta-propeller fold characteristic of
GH (glycoside hydrolase) family 43 and a CBM (carbohydrate-binding module) with
a beta-sandwich fold belonging to CBM family 6. Binding of substrate to
BsAXH-m2,3 is largely based on hydrophobic stacking interactions, which probably
allow the positional flexibility needed to hydrolyse both arabinose substituents
at the O-2 or O-3 position of the xylose unit. Superposition of the BsAXH-m2,3
structure with known structures of the GH family 43 exo-acting enzymes,
beta-xylosidase and alpha-L-arabinanase, each in complex with their substrate,
reveals a different orientation of the sugar backbone.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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S.Kühnel,
Y.Westphal,
S.W.Hinz,
H.A.Schols,
and
H.Gruppen
(2011).
Mode of action of Chrysosporium lucknowense C1 α-l-arabinohydrolases.
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Bioresour Technol,
102,
1636-1643.
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C.S.Park,
M.H.Yoo,
K.H.Noh,
and
D.K.Oh
(2010).
Biotransformation of ginsenosides by hydrolyzing the sugar moieties of ginsenosides using microbial glycosidases.
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Appl Microbiol Biotechnol,
87,
9.
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D.de Sanctis,
J.M.Inácio,
P.F.Lindley,
I.de Sá-Nogueira,
and
I.Bento
(2010).
New evidence for the role of calcium in the glycosidase reaction of GH43 arabinanases.
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FEBS J,
277,
4562-4574.
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PDB codes:
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A.Alhassid,
A.Ben-David,
O.Tabachnikov,
D.Libster,
E.Naveh,
G.Zolotnitsky,
Y.Shoham,
and
G.Shoham
(2009).
Crystal structure of an inverting GH 43 1,5-alpha-L-arabinanase from Geobacillus stearothermophilus complexed with its substrate.
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Biochem J,
422,
73-82.
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PDB codes:
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D.Dodd,
and
I.K.Cann
(2009).
Enzymatic deconstruction of xylan for biofuel production.
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Glob Change Biol Bioenergy,
1,
2.
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R.Carapito,
A.Imberty,
J.M.Jeltsch,
S.C.Byrns,
P.H.Tam,
T.L.Lowary,
A.Varrot,
and
V.Phalip
(2009).
Molecular Basis of Arabinobio-hydrolase Activity in Phytopathogenic Fungi: CRYSTAL STRUCTURE AND CATALYTIC MECHANISM OF FUSARIUM GRAMINEARUM GH93 EXO-{alpha}-L-ARABINANASE.
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J Biol Chem,
284,
12285-12296.
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PDB codes:
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T.K.Attwood,
D.B.Kell,
P.McDermott,
J.Marsh,
S.R.Pettifer,
and
D.Thorne
(2009).
Calling International Rescue: knowledge lost in literature and data landslide!
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Biochem J,
424,
317-333.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
