PDBsum entry 2ehm

Toxin

PDB id

2ehm

Contents

			Protein chains

					283 a.a.

			Ligands

					NGA

			Waters ×555

References listed in PDB file

Key reference

Title

Sugar-Binding sites of the ha1 subcomponent of clostridium botulinum type c progenitor toxin.

Authors

T.Nakamura, T.Tonozuka, A.Ide, T.Yuzawa, K.Oguma, A.Nishikawa.

Ref.

J Mol Biol, 2008, 376, 854-867. [DOI no: 10.1016/j.jmb.2007.12.031]

PubMed id

18178224

Abstract

Clostridium botulinum type C 16S progenitor toxin contains a hemagglutinin (HA) subcomponent, designated HA1, which appears to play an important role in the effective internalization of the toxin in gastrointestinal epithelial cells and in creating a broad specificity for the oligosaccharide structure that corresponds to various targets. In this study, using the recombinant protein fused to glutathione S-transferase, we investigated the binding specificity of the HA1 subcomponent to sugars and estimated the binding sites of HA1 based on X-ray crystallography and soaking experiments using various sugars. N-Acetylneuraminic acid, N-acetylgalactosamine, and galactose effectively inhibited the binding that occurs between glutathione S-transferase-HA1 and mucins, whereas N-acetylglucosamine and glucose did not inhibit it. The crystal structures of HA1 complex with N-acetylneuraminic acid, N-acetylgalactosamine, and galactose were also determined. There are two sugar-binding sites, sites I and II. Site I corresponds to the electron densities noted for all sugars and is located at the C-terminal beta-trefoil domain, while site II corresponds to the electron densities noted only for galactose. An aromatic amino acid residue, Trp176, at site I has a stacking interaction with the hexose ring of the sugars. On the other hand, there is no aromatic residue at site II; thus, the interaction with galactose seems to be poor. The double mutant W176A at site I and D271F at site II has no avidity for N-acetylneuraminic acid but has avidity for galactose. In this report, the binding specificity of botulinum C16S toxin HA1 to various sugars is demonstrated based on its structural features.



	Figure 2. Fig. 2. Three-dimensional structures of HA1–sugar complex and F[o] − F[c] omit maps for the ligands with 2.0 σ contoured level. (a) The overall structure of the HA1–Neu5Ac complex. There are two molecules (Mol-A and Mol-B) in an asymmetric unit; Mol-A and Mol-B are structurally almost identical. HA1 is composed of two β-trefoil domains, N- and C-terminal domains, linked by an α-helix (gray). The three repeats of each domain are displayed in lime green (α-repeat), blue (β-repeat), and magenta (γ-repeat). Two Neu5Ac molecules are indicated by the stick models. The ligands are found at binding sites I and III. At the site I position, Neu5Ac molecules are found not only in Mol-A but also in Mol-B (site I[B]). The binding sites I[A] and I[B] illustrated in the figures are in the equivalent position for each molecule. At the position indicated as binding site III, Neu5Ac is only seen in Mol-A. (b) The HA1–Gal complex structure. Gal molecules are seen at site I[B] located at the 2α-repeat and at site II located at the 2γ-repeat of Mol-B; no electron density for the ligands was observed for Mol-A. The β-strands of 2α- and 2γ-repeat (site I and II) were numbered. (c) The density of Neu5Ac located at binding sites I and III. At binding site I[B], the electron density of the sugar is clearly seen, almost to the same degree as that at binding site I (data not shown). The electron density of Neu5Ac observed at site II is relatively weak. (d) The electron density of GalNAc located at binding site I[B]. (e) The density of Gal located at binding sites I[B] and II[B].		Figure 4. Fig. 4. Superimposed illustrations of the area near the sugar-binding sites of type C and type A HA1. (a) Close-up view of the 2α-repeat region of type C HA1 superimposed on the same region of type A HA1 with a Gal molecule model. The putative sugar-binding residues as observed in type C HA1 (pink) and their counterparts in type A HA1 (blue). Residue labels are indicated for type C HA1; those from the type A HA1 structure are in parentheses. (b) Overlay of the two types of HA1 on the 2γ-repeat region with a stick-modeled Gal.