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PDBsum entry 3vsv
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PDB id:
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Hydrolase
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Title:
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The complex structure of xylc with xylose
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Structure:
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Xylosidase. Chain: a, b, c, d. Synonym: beta-xylosidase. Engineered: yes
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Source:
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Thermoanaerobacterium. Organism_taxid: 60708. Strain: jw/sl ys485. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Resolution:
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1.48Å
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R-factor:
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0.150
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R-free:
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0.168
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Authors:
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C.H.Huang,Y.Sun,T.P.Ko,Y.Ma,C.C.Chen,Y.Zheng,H.C.Chan,X.Pang, J.Wiegel,W.Shao,R.T.Guo
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Key ref:
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C.H.Huang
et al.
(2012).
The substrate/product-binding modes of a novel GH120 β-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485.
Biochem J,
448,
401-407.
PubMed id:
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Date:
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09-May-12
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Release date:
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27-Feb-13
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PROCHECK
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Headers
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References
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A2ICH1
(A2ICH1_THESW) -
Parallel beta-helix repeat protein from Thermoanaerobacterium saccharolyticum (strain DSM 8691 / JW/SL-YS485)
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Seq:
Struc:
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638 a.a.
638 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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Enzyme class:
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E.C.3.2.1.37
- xylan 1,4-beta-xylosidase.
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Reaction:
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Hydrolysis of 1,4-beta-D-xylans so as to remove successive D-xylose residues from the non-reducing termini.
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Biochem J
448:401-407
(2012)
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PubMed id:
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The substrate/product-binding modes of a novel GH120 β-xylosidase (XylC) from Thermoanaerobacterium saccharolyticum JW/SL-YS485.
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C.H.Huang,
Y.Sun,
T.P.Ko,
C.C.Chen,
Y.Zheng,
H.C.Chan,
X.Pang,
J.Wiegel,
W.Shao,
R.T.Guo.
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ABSTRACT
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Xylan-1,4-β-xylosidase (β-xylosidase) hydrolyses xylo-oligomers at their
non-reducing ends into individual xylose units. Recently, XylC, a β-xylosidase
from Thermoanaerobacterium saccharolyticum JW/SL-YS485, was found to be
structurally different from corresponding glycosyl hydrolases in the CAZy
database (http://www.cazy.org/), and was subsequently classified as the first
member of a novel family of glycoside hydrolases (GH120). In the present paper,
we report three crystal structures of XylC in complex with Tris, xylobiose and
xylose at 1.48-2.05 Å (1 Å=0.1 nm) resolution. XylC assembles into a tetramer,
and each monomer comprises two distinct domains. The core domain is a
right-handed parallel β-helix (residues 1-75 and 201-638) and the flanking
region (residues 76-200) folds into a β-sandwich domain. The enzyme contains an
open carbohydrate-binding cleft, allowing accommodation of longer
xylo-oligosaccharides. On the basis of the crystal structures and in agreement
with previous kinetic data, we propose that XylC cleaves the glycosidic bond by
the retaining mechanism using two acidic residues Asp382 (nucleophile) and
Glu405 (general acid/base). In addition to the active site, nine other
xylose-binding sites were consistently observed in each of the four monomers,
providing a possible reason for the high tolerance of product inhibition.
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