PDBsum entry 1c58

Carbohydrate

PDB id: 1c58

Contents

Ligands

GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC-GLC ×2

Waters ×147

PDB id:

1c58

Name:

Carbohydrate

Title:

Crystal structure of cycloamylose 26

Structure:

Cyclohexacosakis-(1-4)-(alpha-d-glucopyranose). Chain: a, b. Engineered: yes

Source:

not given

Resolution:

0.99Å R-factor: 0.082 R-free: 0.100

Authors:

K.Gessler,W.Saenger,O.Nimz

Key ref:

K.Gessler et al. (1999). V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose). Proc Natl Acad Sci U S A, 96, 4246-4251. PubMed id: 10200247 DOI: 10.1073/pnas.96.8.4246

Date:

04-Nov-99 Release date: 10-Nov-99

DOI no: 10.1073/pnas.96.8.4246

Proc Natl Acad Sci U S A 96:4246-4251 (1999)

PubMed id: 10200247

V-Amylose at atomic resolution: X-ray structure of a cycloamylose with 26 glucose residues (cyclomaltohexaicosaose).

K.Gessler, I.Usón, T.Takaha, N.Krauss, S.M.Smith, S.Okada, G.M.Sheldrick, W.Saenger.

ABSTRACT

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.

Selected figure(s)

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).

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).

Figures were selected by an automated process.