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PDBsum entry 1h4h
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Glycoside hydrolase
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PDB id
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1h4h
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Catalysis and specificity in enzymatic glycoside hydrolysis: a 2,5b conformation for the glycosyl-Enzyme intermediate revealed by the structure of the bacillus agaradhaerens family 11 xylanase.
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Authors
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E.Sabini,
G.Sulzenbacher,
M.Dauter,
Z.Dauter,
P.L.Jørgensen,
M.Schülein,
C.Dupont,
G.J.Davies,
K.S.Wilson.
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Ref.
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Chem Biol, 1999,
6,
483-492.
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PubMed id
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Abstract
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BACKGROUND: The enzymatic hydrolysis of glycosides involves the formation and
subsequent breakdown of a covalent glycosyl-enzyme intermediate via
oxocarbenium-ion-like transition states. The covalent intermediate may be
trapped on-enzyme using 2-fluoro-substituted glycosides, which provide details
of the intermediate conformation and noncovalent interactions between enzyme and
oligosaccharide. Xylanases are important in industrial applications - in the
pulp and paper industry, pretreating wood with xylanases decreases the amount of
chlorine-containing chemicals used. Xylanases are structurally similar to
cellulases but differ in their specificity for xylose-based, versus
glucose-based, substrates. RESULTS: The structure of the family 11 xylanase,
Xyl11, from Bacillus agaradhaerens has been solved using X-ray crystallography
in both native and xylobiosyl-enzyme intermediate forms at 1.78 A and 2.0 A
resolution, respectively. The covalent glycosyl-enzyme intermediate has been
trapped using a 2-fluoro-2-deoxy substrate with a good leaving group. Unlike
covalent intermediate structures for glycoside hydrolases from other families,
the covalent glycosyl-enzyme intermediate in family 11 adopts an unusual 2,5B
conformation. CONCLUSIONS: The 2,5B conformation found for the alpha-linked
xylobiosyl-enzyme intermediate of Xyl11, unlike the 4C1 chair conformation
observed for other systems, is consistent with the stereochemical constraints
required of the oxocarbenium-ion-like transition state. Comparison of the Xyl11
covalent glycosyl-enzyme intermediate with the equivalent structure for the
related family 12 endoglucanase, CelB, from Streptomyces lividans reveals the
likely determinants for substrate specificity in this clan of glycoside
hydrolases.
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Added reference #1*
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Title
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Oligosaccharide binding to family 11 xylanases: both covalent intermediate and mutant product complexes display (2,5)B conformations at the active centre.
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Authors
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E.Sabini,
K.S.Wilson,
S.Danielsen,
M.Schülein,
G.J.Davies.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
1344-1347.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Interactions of the Xyn11 E94A mutant with xylotriose.
The -1 subsite of the covalent 2-fluoro-2-deoxyxylobiosyl-enzyme
intermediate (Sabini et al., 1999[Sabini, E., Sulzenbacher, G.,
Dauter, M., Dauter, Z., Jørgensen, P. L., Schülein, M., Dupont,
C., Davies, G. J. & Wilson, K. S. (1999). Chem. Biol. 6,
483-492.]) is included for reference.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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*Note, "added" references are those not in the PDB file but
which have either been obtained from the journal or suggested by the
author(s).
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