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PDBsum entry 1v6w
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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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Crystal structures of decorated xylooligosaccharides bound to a family 10 xylanase from streptomyces olivaceoviridis e-86.
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Authors
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Z.Fujimoto,
S.Kaneko,
A.Kuno,
H.Kobayashi,
I.Kusakabe,
H.Mizuno.
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Ref.
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J Biol Chem, 2004,
279,
9606-9614.
[DOI no: ]
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PubMed id
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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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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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