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PDBsum entry 1v6v
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* Residue conservation analysis
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Enzyme class:
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E.C.3.2.1.8
- endo-1,4-beta-xylanase.
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Reaction:
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Endohydrolysis of 1,4-beta-D-xylosidic linkages in xylans.
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DOI no:
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J Biol Chem
279:9606-9614
(2004)
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PubMed id:
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Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from Streptomyces olivaceoviridis E-86.
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Z.Fujimoto,
S.Kaneko,
A.Kuno,
H.Kobayashi,
I.Kusakabe,
H.Mizuno.
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ABSTRACT
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The family 10 xylanase from Streptomyces olivaceoviridis E-86 (SoXyn10A)
consists of a GH10 catalytic domain, which is joined by a Gly/Pro-rich linker to
a family 13 carbohydrate-binding module (CBM13) that interacts with xylan. To
understand how GH10 xylanases and CBM13 recognize decorated xylans, the crystal
structure of SoXyn10A was determined in complex with alpha-l-arabinofuranosyl-
and 4-O-methyl-alpha-d-glucuronosyl-xylooligosaccharides. The bound sugars were
observed in the subsites of the catalytic cleft and also in subdomains alpha and
gamma of CBM13. The data reveal that the binding mode of the oligosaccharides in
the active site of the catalytic domain is entirely consistent with the
substrate specificity and, in conjunction with the accompanying paper,
demonstrate that the accommodation of the side chains in decorated xylans is
conserved in GH10 xylanases of SoXyn10A against arabinoglucuronoxylan. CBM13 was
shown to bind xylose or xylooligosaccharides reversibly by using nonsymmetric
sugars as the ligands. The independent multiple sites in CBM13 may increase the
probability of substrate binding.
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Selected figure(s)
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Figure 2.
FIG. 2. Stereo view of the bound decorated
xylooligosaccharides in the catalytic cleft, with the F[obs] -
F[calc] omit electron density maps contoured at 2.5  for the
decorated xylooligosaccharides in the (-) side of the cleft. A,
SoXyn10A·Araf-X3 complex. B, SoXyn10A·MeGlcUA-X3
complex. Hydrogen bonding interactions between the enzyme and
sugars are indicated by broken lines.
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Figure 6.
FIG. 6. Stereo views of Araf-X3. A, Araf-X3 bound in the
catalytic cleft; B, Araf-X3 bound in subdomain  of
SoCBM13, with the F[obs] - F[calc] omit electron density maps
contoured at 2.5 . The intramolecular
hydrogen bond is shown as a broken line.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2004,
279,
9606-9614)
copyright 2004.
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Figures were
selected
by an automated process.
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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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A.Pollet,
J.A.Delcour,
and
C.M.Courtin
(2010).
Structural determinants of the substrate specificities of xylanases from different glycoside hydrolase families.
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Crit Rev Biotechnol,
30,
176-191.
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O.Gallardo,
F.I.Pastor,
J.Polaina,
P.Diaz,
R.Łysek,
P.Vogel,
P.Isorna,
B.González,
and
J.Sanz-Aparicio
(2010).
Structural insights into the specificity of Xyn10B from Paenibacillus barcinonensis and its improved stability by forced protein evolution.
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J Biol Chem,
285,
2721-2733.
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PDB codes:
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S.Anbarasan,
J.Jänis,
M.Paloheimo,
M.Laitaoja,
M.Vuolanto,
J.Karimäki,
P.Vainiotalo,
M.Leisola,
and
O.Turunen
(2010).
Effect of glycosylation and additional domains on the thermostability of a family 10 xylanase produced by Thermopolyspora flexuosa.
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Appl Environ Microbiol,
76,
356-360.
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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.Suzuki,
Z.Fujimoto,
S.Ito,
S.Kawahara,
S.Kaneko,
K.Taira,
T.Hasegawa,
and
A.Kuno
(2009).
Crystallographic snapshots of an entire reaction cycle for a retaining xylanase from Streptomyces olivaceoviridis E-86.
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J Biochem,
146,
61-70.
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PDB codes:
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C.B.Faulds,
G.Mandalari,
R.B.Lo Curto,
G.Bisignano,
P.Christakopoulos,
and
K.W.Waldron
(2006).
Synergy between xylanases from glycoside hydrolase family 10 and family 11 and a feruloyl esterase in the release of phenolic acids from cereal arabinoxylan.
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Appl Microbiol Biotechnol,
71,
622-629.
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F.J.Stjohn,
J.D.Rice,
and
J.F.Preston
(2006).
Paenibacillus sp. strain JDR-2 and XynA1: a novel system for methylglucuronoxylan utilization.
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Appl Environ Microbiol,
72,
1496-1506.
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Ihsanawati,
T.Kumasaka,
T.Kaneko,
C.Morokuma,
R.Yatsunami,
T.Sato,
S.Nakamura,
and
N.Tanaka
(2005).
Structural basis of the substrate subsite and the highly thermal stability of xylanase 10B from Thermotoga maritima MSB8.
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Proteins,
61,
999.
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PDB codes:
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M.Nishimoto,
M.Kitaoka,
S.Fushinobu,
and
K.Hayashi
(2005).
The role of conserved arginine residue in loop 4 of glycoside hydrolase family 10 xylanases.
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Biosci Biotechnol Biochem,
69,
904-910.
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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
