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PDBsum entry 1vbu
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References listed in PDB file
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Key reference
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Title
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Structural basis of the substrate subsite and the highly thermal stability of xylanase 10b from thermotoga maritima msb8.
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Authors
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Ihsanawati,
T.Kumasaka,
T.Kaneko,
C.Morokuma,
R.Yatsunami,
T.Sato,
S.Nakamura,
N.Tanaka.
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Ref.
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Proteins, 2005,
61,
999.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of xylanase 10B from Thermotoga maritima MSB8 (TmxB), a
hyperthermostable xylanase, has been solved in its native form and in complex
with xylobiose or xylotriose at 1.8 A resolution. In order to gain insight into
the substrate subsite and the molecular features for thermal stability, we
compared TmxB with family 10 xylanase structures from nine microorganisms. As
expected, TmxB folds into a (beta/alpha)8-barrel structure, which is common
among the glycoside hydrolase family 10. The enzyme active site and the
environment surrounding the xylooligosaccharide of TmxB are highly similar to
those of family 10 xylanases. However, only two xylose moieties were found in
its binding pocket from the TmxB-xylotriose complex structure. This finding
suggests that TmxB could be a potential biocatalyst for the large-scale
production of xylobiose. The result of structural analyses also indicated that
TmxB possesses some additional features that account for its thermostability. In
particular, clusters of aromatic residues together with a lack of exposed
hydrophobic residues are characteristic of the TmxB structure. TmxB has also a
significant number of ion pairs on the protein surface that are not found in
other thermophilic family 10 xylanases.
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Figure 1.
Figure 1. A: Overall structure of TmxB (in stereo) from the top
view. Major  -helices
and  -strands
are drawn in red and green, respectively, and labeled according
to the ideal ( /
)[8]
barrel structure.[42] The two catalytic residues are labeled and
depicted by ball-and-stick facing two xylose moieties. B: Stereo
view of superimposition of TmxB-xylotriose (yellow) with
Psx-xylotriose (blue) in the catalytic site. Red dash lines
indicate hydrogen bonds in the TmxB complex structure, which are
also found in Psx. Blue dash lines represent hydrogen bonds,
which are only found in Psx.
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Figure 4.
Figure 4. Molecular interactions for thermal stability of TmxB.
A: Aromatic interactions from the top view showing five distinct
clusters drawn in different colors. B: Electrostatic
interactions in the C-terminal region consist of a triad salt
bridge (Asp780-Asp784-Lys836) and single ones (Lys769-Glu773,
Asp798-Lys823 and Lys835-Glu839. C-E: Comparison of aromatic
interactions, connecting 1,
2,
1,
and 8
in TmxB, Ctx, and Pfx, respectively.
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2005,
61,
999-0)
copyright 2005.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray studies of xylanase 10b from thermotoga maritima.
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Authors
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Ihsanawati,
T.Kumasaka,
T.Kaneko,
C.Morokuma,
S.Nakamura,
N.Tanaka.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2003,
59,
1659-1661.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 Crystals of xylanase 10B (a) from the initial
conditions and (b) after optimization.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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