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PDBsum entry 1isw
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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 the sugar complexes of streptomyces olivaceoviridis e-86 xylanase: sugar binding structure of the family 13 carbohydrate binding module.
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Authors
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Z.Fujimoto,
A.Kuno,
S.Kaneko,
H.Kobayashi,
I.Kusakabe,
H.Mizuno.
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Ref.
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J Mol Biol, 2002,
316,
65-78.
[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 contains a
(beta/alpha)(8)-barrel as a catalytic domain, a family 13 carbohydrate binding
module (CBM) as a xylan binding domain (XBD) and a Gly/Pro-rich linker between
them. The crystal structure of this enzyme showed that XBD has three similar
subdomains, as indicated by the presence of a triple-repeated sequence, forming
a galactose binding lectin fold similar to that found in the ricin toxin
B-chain. Comparison with the structure of ricin/lactose complex suggests three
potential sugar binding sites in XBD. In order to understand how XBD binds to
the xylan chain, we analyzed the sugar-complex structure by the soaking
experiment method using the xylooligosaccharides and other sugars. In the
catalytic cleft, bound sugars were observed in the xylobiose and xylotriose
complex structures. In the XBD, bound sugars were identified in subdomains alpha
and gamma in all of the complexes with xylose, xylobiose, xylotriose, glucose,
galactose and lactose. XBD binds xylose or xylooligosaccharides at the same
sugar binding sites as in the case of the ricin/lactose complex but its binding
manner for xylose and xylooligosaccharides is different from the galactose
binding mode in ricin, even though XBD binds galactose in the same manner as in
the ricin/galactose complex. These different binding modes are utilized
efficiently and differently to bind the long substrate to xylanase and
ricin-type lectin. XBD can bind any xylose in the xylan backbone, whereas
ricin-type lectin recognizes the terminal galactose to sandwich the large sugar
chain, even though the two domains have the same family 13 CBM structure. Family
13 CBM has rather loose and broad sugar specificities and is used by some kinds
of proteins to bind their target sugars. In such enzyme, XBD binds xylan, and
the catalytic domain may assume a flexible position with respect to the
XBD/xylan complex, inasmuch as the linker region is unstructured.
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Figure 1.
Figure 1. Stereo view of the ribbon model of FXYN/X2
complex. The catalytic domain, linker, and subdomains a, b, g of
XBD are drawn in green, black, blue, yellow and pink,
respectively. Two catalytic residues are displayed in red.
Soaked xylose units and disulfide bonds are indicated by
ball-and-stick drawings. The figure was drawn with the program
Raster3d.[46 and 47]
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Figure 5.
Figure 5. Stereo views of the sugar binding structures in
the XBD with the F[obs] - F[calc] omit electron density maps
contoured at 3s. (a) In the subdomain a in the FXYN/X2 complex,
(b) subdomain g in the FXYN/X3 complex, (c) subdomain g in the
FXYN/Glc complex, (d) subdomain a in the FXYN/Gal complex, (e)
subdomain g in the FXYN/Lac complex, and (f) subdomain a in the
FXYN/Lac complex from a different view point. Hydrogen bonding
interactions between the enzyme and sugars are indicated by
broken lines. Carbon numbers of bound xylose are indicated.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2002,
316,
65-78)
copyright 2002.
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Secondary reference #1
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Title
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Crystal structure of streptomyces olivaceoviridis e-86 beta-Xylanase containing xylan-Binding domain.
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Authors
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Z.Fujimoto,
A.Kuno,
S.Kaneko,
S.Yoshida,
H.Kobayashi,
I.Kusakabe,
H.Mizuno.
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Ref.
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J Mol Biol, 2000,
300,
575-585.
[DOI no: ]
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PubMed id
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Figure 6.
Figure 6. Stereoview of xylotriose docking model in
subdomain b of XBD. The xylotriose structure was built based on
the X-ray structure of b-1,4-xylan hydrate [Neduszynski and
Marchessault 1972] and fitted into the binding site manually.
Sugars are numbered from the non-reducing end. XBD residues
interact with the 2nd xylose sugar through five hydrogen bonds
(broken lines). The 2nd and 3rd sugar rings are placed over the
aromatic rings of Tyr380 and Trp383.
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Figure 7.
Figure 7. Stereoview of an interacting region between the
catalytic domain (green) and XBD (subdomains a, blue; b, yellow;
g, pink) superimposed on the equivalent region of the catalytic
domain in Cex (white; 2exo; [White et al 1994]). Five inferred
hydrogen bonding interactions between the triple Ser sequence in
the N-terminal end of Ca7 and Asp354 in XBD are shown as blue
broken lines. The difference between FXYN and Cex is clearly
seen in the region from Cb7 to Ca7.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Crystallization and preliminary X-Ray crystallographic study of streptomyces olivaceoviridis e-86 beta-Xylanase.
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Authors
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Z.Fujimoto,
H.Mizuno,
A.Kuno,
S.Yoshida,
H.Kobayashi,
I.Kusakabe.
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Ref.
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J Biochem (tokyo), 1997,
121,
826-828.
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PubMed id
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