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PDBsum entry 1kum
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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 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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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
92%.
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Abstract
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The solution structure of the granular starch binding domain (SBD) of
glucoamylase 1 from Aspergillus niger has been determined by heteronuclear
multidimensional nuclear magnetic resonance spectroscopy and simulated
annealing. A total of 1092 nuclear Overhauser enhancement-derived 1H-1H distance
constraints, 137 dihedral constraints and 86 hydrogen bond constraints were
incorporated into an X-PLOR simulated annealing and refinement protocol. The
family of calculated structures shows a well defined beta-sheet structure
consisting of one parallel and six antiparallel pairs of beta-strands which
forms an open-sided beta-barrel. The root-mean-square deviation (rmsd) of 53
individual structures to the calculated average structure for the backbone atoms
of residues excluding the N terminus and two mobile loops is 0.57(+/-0.10) A
while the rmsd for backbone atoms in beta-strands is 0.45(+/-0.08) A. Structural
features of the SBD in solution are compared to the X-ray crystal structure of a
homologous domain of cyclodextrin glycosyltransferase (CGTase) in the free and
bound forms. Titration studies with two ligands, maltoheptaose and
beta-cyclodextrin, show the existence of two binding sites. Examination of the
tertiary structures shows these two sites to be at one end of the molecule on
opposite faces. The majority of residues showing the largest 1H and 15N chemical
shift changes are located in loop regions. Many residues implicated in binding,
based on these changes, are similar in location to previously identified binding
site residues in the crystal structures of CGTase. Overall, the shift changes
are small indicating that the SBD does not undergo large conformational changes
upon ligand binding.
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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
reprinted
by permission from Elsevier:
J Mol Biol
(1996,
259,
970-987)
copyright 1996.
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Secondary reference #1
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Title
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1h and 15n assignments and secondary structure of the starch-Binding domain of glucoamylase from aspergillus niger.
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Authors
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A.J.Jacks,
K.Sorimachi,
M.F.Le gal-Coëffet,
G.Williamson,
D.B.Archer,
M.P.Williamson.
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Ref.
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Eur J Biochem, 1995,
233,
568-578.
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PubMed id
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