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PDBsum entry 1c58
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References listed in PDB file
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Key reference
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Title
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V-Amylose at atomic resolution: X-Ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose).
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Authors
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K.Gessler,
I.Usón,
T.Takaha,
N.Krauss,
S.M.Smith,
S.Okada,
G.M.Sheldrick,
W.Saenger.
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Ref.
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Proc Natl Acad Sci U S A, 1999,
96,
4246-4251.
[DOI no: ]
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PubMed id
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Abstract
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The amylose fraction of starch occurs in double-helical A- and B-amyloses and
the single-helical V-amylose. The latter contains a channel-like central cavity
that is able to include molecules, "iodine's blue" being the
best-known representative. Molecular models of these amylose forms have been
deduced by solid state 13C cross-polarization/magic angle spinning NMR and by
x-ray fiber and electron diffraction combined with computer-aided modeling. They
remain uncertain, however, as no structure at atomic resolution is available. We
report here the crystal structure of a hydrated cycloamylose containing 26
glucose residues (cyclomaltohexaicosaose, CA26), which has been determined by
real/reciprocal space recycling starting from randomly positioned atoms or from
an oriented diglucose fragment. This structure provides conclusive evidence for
the structure of V-amylose, as the macrocycle of CA26 is folded into two short
left-handed V-amylose helices in antiparallel arrangement and related by twofold
rotational pseudosymmetry. In the V-helices, all glucose residues are in syn
orientation, forming systematic interglucose O(3)n...O(2)(n+l) and
O(6)n...O(2)(n+6)/O(3)(n+6) hydrogen bonds; the central cavities of the
V-helices are filled by disordered water molecules. The folding of the CA26
macrocycle is characterized by typical "band-flips" in which
diametrically opposed glucose residues are in anti rather than in the common syn
orientation, this conformation being stabilized by interglucose three-center
hydrogen bonds with O(3)n as donor and O(5)(n+l), O(6)(n+l) as acceptors. The
structure of CA26 permitted construction of an idealized V-amylose helix, and
the band-flip motif explains why V-amylose crystallizes readily and may be
packed tightly in seeds.
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Figure 1.
Fig. 1. Two sections of electron density at 1.0-Å
resolution. (A) Segment of four glucoses, G25 to G2, showing one
of the two bandflip sites in CA26 defined by G26-G1; these two
glucoses are stabilized in anti orientation by the three-center
hydrogen bond
O(3)[26]---H···(O(5)[1],O(6)[1]. The
adjacent glucoses on both sides of the flip are oriented syn as
usually found in amylose chains and hydrogen bonded
O(3)[n]···O(2)[n+1]. Because the flip at
G26-G1 involves not just a single glucose but the whole appended
amylose chain, it was called "band-flip" (18). Labels of O(2)
and O(3) hydroxyl groups are circled to emphasize the abrupt
structural change at the band-flip site. (B) Disordered water
molecules located in the channel-like cavity of the V-amylose
helix. Because the distances between their positions (marked *)
are shorter than the minimum hydrogen bonding distance of 2.5
Å (30), the occupations are around 0.5. Drawn with O (31).
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Figure 3.
Fig. 3. (Left) View of CA26, molecule A. Those parts of
the molecule located at the front are light gray, those at the
back dark; glucose residues G are numbered 1-26. Curved arrows
indicate the "directions" of the two V-helices. The location of
the pseudo-twofold rotation axis (  ) is
between water molecules W1 and W2 and vertical to the plane of
the paper. Disordered water molecules filling the channel-like
cavities in the two V-helical segments are shown in red, as are
two five-coordinated water molecules, W1 and W2, in strategic
positions conferring stability to the folding of CA26. They are
hydrogen bonded in bidentate mode to O5/O6 atoms; W1 to G21 and
G2; W2 to G8 and G15, with additional single hydrogen bonds
W1···O(2)[8] and
W2···O(2)[21]. Water molecules W3 and W4
are not shown, as they are at the "back" of the molecule and
nearly overlap with W1 and W2. (Right) View as in Left, but
rotated 90° so that the pseudo-twofold axis (blue arrow) is
now horizontal. Shown is the interface between the two V-helices
where the band-flip segments, glucoses G26-G1 and G13-G14, are
connected by direct and water (W3 and W4)-mediated hydrogen
bonds to glucoses G7 and G20. Note superposition of G7 on G20,
forming part of the interface between the V-helices. Oxygen
atoms of glucose 1 are labeled. Drawn with INSIGHT II (32).
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Headers
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