2-Acetamido-2-de­oxy-3-O-β-d-galactopyranosyl-d-glucose dihydrate

Masahisa Wada; Kayoko Kobayashi; Mamoru Nishimoto; Motomitsu Kitaoka; Keiichi Noguchi

doi:10.1107/S1600536809024775

. 2009 Jul 4;65(Pt 8):o1781–o1782. doi: 10.1107/S1600536809024775

2-Acetamido-2-deoxy-3-O-β-d-galactopyranosyl-d-glucose dihydrate

Masahisa Wada ^a,^*, Kayoko Kobayashi ^a, Mamoru Nishimoto ^b, Motomitsu Kitaoka ^b, Keiichi Noguchi ^c

PMCID: PMC2977301 PMID: 21583488

Abstract

In the title compound, C₁₄H₂₅NO₁₁·2H₂O, the primary hydroxyl group connected to the anomeric C atom of the N-acetyl-β-d-glucopyranose residue exhibits positional disorder, with occupancy factors for the α and β anomers of 0.77 and 0.23, respectively. The two torsion angles (Φ and Ψ) and the bridge angle (τ) that describe conformation of the glycosidic linkage between the galactopyranose and glucopyranose rings are Φ = −81.6 (3)°, Ψ = 118.1 (2)° and τ = 115.2 (2)°. Two water molecules stabilize the molecular packing by forming hydrogen bonds with the saccharide residues.

Related literature

For the synthesis of the title compound, see: Kitaoka et al. (2005 ▶); Nishimoto & Kitaoka (2007a ▶,b ▶). For the conformation of saccharide rings, see: Cremer & Pople (1975 ▶).

Experimental

Crystal data

C₁₄H₂₅NO₁₁·2H₂O
M _r = 419.38
Orthorhombic,
a = 8.284 (1) Å
b = 12.841 (1) Å
c = 17.503 (1) Å
V = 1861.9 (3) Å³
Z = 4
Synchrotron radiation
λ = 0.80000 Å
μ = 0.13 mm⁻¹
T = 95 K
0.10 × 0.10 × 0.10 mm

Data collection

ADSC Quantum 210r diffractometer
Absorption correction: none
25787 measured reflections
2153 independent reflections
2046 reflections with I > 2σ(I)
R _int = 0.047

Refinement

R[F ² > 2σ(F ²)] = 0.042
wR(F ²) = 0.115
S = 1.06
2153 reflections
264 parameters
H-atom parameters constrained
Δρ_max = 0.27 e Å⁻³
Δρ_min = −0.31 e Å⁻³

Data collection: UGUI (Structural Biology Research Center, 2005 ▶); cell refinement: HKL-2000 (Otwinowski & Minor, 1997 ▶); data reduction: HKL-2000; program(s) used to solve structure: SHELXS86 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEPIII (Burnett & Johnson, 1996 ▶); software used to prepare material for publication: SHELXL97.

Supplementary Material

Crystal structure: contains datablocks global, I. DOI: 10.1107/S1600536809024775/is2433sup1.cif

e-65-o1781-sup1.cif^{(23.4KB, cif)}

Structure factors: contains datablocks I. DOI: 10.1107/S1600536809024775/is2433Isup2.hkl

e-65-o1781-Isup2.hkl^{(103.7KB, hkl)}

Additional supplementary materials: crystallographic information; 3D view; checkCIF report

Table 1. Selected bond and torsion angles (°).

C1—O1—C9

115.2 (2)

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O5—C1—O1—C9	−81.6 (3)
C2—C1—O1—C9	159.0 (2)
C1—O1—C9—C10	118.0 (2)
C1—O1—C9—C8	−123.3 (2)

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Table 2. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
N1—H1N⋯O2Wⁱ	0.88	2.05	2.923 (3)	169
O2—H2O⋯O12ⁱⁱ	0.85	1.80	2.642 (3)	170
O3—H3O⋯O2W	0.85	1.86	2.702 (3)	169
O4—H4O⋯O13ⁱⁱ	0.93	1.95	2.803 (3)	150
O6—H6O⋯O1Wⁱⁱⁱ	0.85	1.79	2.624 (3)	168
O10—H10O⋯O6^iv	0.96	1.81	2.705 (3)	154
O1W—H11W⋯O10^iv	0.85	1.85	2.696 (3)	175
O12—H12O⋯O13^v	0.85	1.96	2.784 (3)	162
O1W—H12W⋯O4	0.87	1.90	2.759 (3)	173
O2W—H21W⋯O11^vi	0.90	1.94	2.772 (3)	154
O2W—H22W⋯O6^vii	0.85	1.91	2.757 (3)	171
O71—H71O⋯O2ⁱ	0.86	1.87	2.683 (3)	159
O72—H72O⋯O1W^v	0.84	2.04	2.545 (9)	119

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Symmetry codes: (i) Inline graphic ; (ii) ; (iii) ; (iv) ; (v) ; (vi) ; (vii) .

Acknowledgments

This study was supported in part by a grant from the Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) of Japan.

supplementary crystallographic information

Comment

It is widely accepted that oligosaccharides other than lactose in human milk (human milk oligosaccharides, HMOs) play a key role in the growth of Bifidobacteria in the gut. Bifidobacteria, Gram-positive anaerobes, are considered to be beneficial for human health. Recently, a unique metabolic pathway specific for lacto-N-biose I (Gal-β1→3GlcNAc, LNB) was found using Bifidobacteria (Kitaoka et al., 2005; Nishimoto & Kitaoka, 2007a). LNB is one of the basic core disaccharides of HMOs and is suggested to be a bifidus factor.

The molecular structure of compound (I) is shown in Fig. 1. There are two water molecules per LNB molecule in the crystal lattice. The primary hydroxyl group connected to the anomeric carbon atom of the GlcNAc residue exhibits disorder, with occupancy factors of O71 (α anomer) and O72 (β anomer) of 0.77 and 0.23, respectively.

The Gal ring is close to the ideal ⁴C₁ chair conformation with ring puckering parameters (Cremer & Pople, 1975) of Q = 0.556 (3) Å, Θ = 7.1 (3)° and Φ = 353 (2)° for the atom sequence O5—C1—C2—C3—C4—C5. The other GlcNAc ring is also close to the ideal chair conformation, with Q = 0.618 (3) Å, Θ = 3.8 (3)°, and Φ = 198 (4)° for the atom sequence O11—C7—C8—C9—C10—C11.

The conformation about the linkage between the Gal and GlcNAc rings is characterized by the torsion angles of Φ (O5—C1—O1—C9) and Ψ (C1—O1—C9—C10), and the bridge angle τ (C1—O1—C9). The values obtained in this study are Φ = -81.6 (3)°, Ψ = 118.1 (2)° and τ = 115.2 (2)° (Table 1).

The conformation of the hydroxymethyl group is defined by two sets of torsion angle: χ and χ'. The values for the Gal ring were χ (O5—C5—C6—O6) = 79.5 (3)° and χ' (C4—C5—C6—O6) = -157.9 (2)°, indicating values close to the gt conformation. The values for the GlcNAc ring are χ (O11—C11—C12—O12) = -64.1 (3)° and χ' (C10—C11—C12—O12) = 57.9 (3)°, indicating the gg conformation.

Both saccharide rings lie approximately parallel to the bc plane and the intermolecular hydrogen bonds were only along the a-axis (Table 2). Two water molecules stabilize the molecular packing by forming hydrogen bonds with sugar molecules in three dimensions.

Experimental

Compound (I) was synthesized from sucrose and GlcNAc by the concurrent action of four enzymes: sucrose phosphorylase, UDP-glucose-hexose-1-phosphate uridylyltransferase, UDP-glucose 4-epimerase, and lacto-N-biose phosphorylase (Nishimoto & Kitaoka, 2007b). Single crystals suitable for X-ray analysis were obtained by slow diffusion of ethanol into an aqueous solution.