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PDBsum entry 1ac0
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References listed in PDB file
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Key reference
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Title
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Solution structure of the granular starch binding domain of aspergillus niger glucoamylase bound to beta-Cyclodextrin.
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Authors
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K.Sorimachi,
M.F.Le gal-Coëffet,
G.Williamson,
D.B.Archer,
M.P.Williamson.
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Ref.
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Structure, 1997,
5,
647-661.
[DOI no: ]
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PubMed id
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Note In the PDB file this reference is
annotated as "TO BE PUBLISHED".
The citation details given above were identified by an automated
search of PubMed on title and author
names, giving a
percentage match of
90%.
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Abstract
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BACKGROUND: Carbohydrate-binding domains are usually small and physically
separate from the catalytic domains of hydrolytic enzymes. Glucoamylase 1 (G1)
from Aspergillus niger, an enzyme used widely in the food and brewing
industries, contains a granular starch binding domain (SBD) which is separated
from the catalytic domain by a semi-rigid linker. The aim of this study was to
determine how the SBD binds to starch, and thereby more generally to throw light
on the role of carbohydrate-binding domains in the hydrolysis of insoluble
polysaccharides. RESULTS: The solution structure of the SBD of A. niger G1 bound
to beta-cyclodextrin (betaCD), a cyclic starch analogue, shows that the
well-defined beta-sheet structure seen in the free SBD is maintained in the
SBD-betaCD complex. The main differences between the free and bound states of
the SBD are observed in loop regions, in or near the two starch-binding sites.
The two binding sites, each of which binds one molecule of betaCD, are
structurally different. Binding site 1 is small and accessible, and its
structure changes very little upon ligand binding. Site 2 is longer and
undergoes a significant structural change on binding. Part of this site
comprises a flexible loop, which appears to allow the SBD to bind to starch
strands in a range of orientations. CONCLUSIONS: The two starch-binding sites of
the SBD probably differ functionally as well as structurally; site 1 probably
acts as the initial starch recognition site, whereas site 2 is involved in
specific recognition of appropriate regions of starch. The two starch strands
are bound at approximately 90 degrees to each other. This may be functionally
important, as it may force starch strands apart thus increasing the hydrolyzable
surface, or alternatively it may localize the enzyme to noncrystalline (more
hydrolyzable) areas of starch. The region of the SBD where the linker to the
catalytic domain is attached is flexible, allowing the catalytic site to access
a large surface area of the starch granules.
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Figure 7.
Figure 7. A view of the superimposition of SBD-bCD[av-min]
(red) and the minimized average structure of free SBD (blue).
The structure of free SBD was superimposed on to the N, Ca and C
atoms of b strands 1-8 of SBD-bCD[av-min]. The bCD molecules are
shown in yellow.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
647-661)
copyright 1997.
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Secondary reference #1
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Title
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Solution structure of the granular starch binding domain of glucoamylase from aspergillus niger by nuclear magnetic resonance spectroscopy.
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Authors
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K.Sorimachi,
A.J.Jacks,
M.F.Le gal-Coëffet,
G.Williamson,
D.B.Archer,
M.P.Williamson.
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Ref.
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J Mol Biol, 1996,
259,
970-987.
[DOI no: ]
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PubMed id
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Figure 4.
Figure 4. Representation of the solution structure of the
SBD. The N and C termini and b-strand numbers are
marked. The strands are shown as arrows which also
indicate their directionality. The atomic coordinates of
SBDav-min were used and the molecule was oriented by eye
to give the best view of the b-strands. The orientation is
rotated by approximately 180° about the vertical axis
compared to Figure 3. The Figure was generated using
the program MOLSCRIPT (Kraulis, 1991). The position of
the disulphide bond is highlighted by ball figures for S
g
atoms and lines for C
a
-C
b
, C
b
-S
g
(both intraresidue) and
S
g
-S
g
(interresidue) bonds for residues 509 and 604.
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Figure 5.
Figure 5. Representation of the
direction and alignment of the
b-strands (numbered 1 to 8) in SBD.
The first and last residues in each
strand are marked at the ends of the
arrows.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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