PDBsum entry: 3ef2

Sugar binding protein

PDB id: 3ef2

Contents

Protein chains

292 a.a. *

Ligands

FUC-GAL-GLA ×8

FUC-GLA-GLA ×4

ACT ×4

Metals

_CA ×16

Waters ×1258

* Residue conservation analysis

PDB id:

3ef2

Name:

Sugar binding protein

Title:

Structure of the marasmius oreades mushroom lectin (moa) in complex with galalpha(1,3)[fucalpha(1,2)]gal and calcium.

Structure:

Agglutinin. Chain: a, b, c, d. Synonym: lectin. Engineered: yes

Source:

Marasmius oreades. Organism_taxid: 181124. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

1.80Å R-factor: 0.166 R-free: 0.189

Authors:

E.M.Grahn,I.J.Goldstein,U.Krengel

Key ref:

E.M.Grahn et al. (2009). Structural Characterization of a Lectin from the Mushroom Marasmius oreades in Complex with the Blood Group B Trisaccharide and Calcium. J Mol Biol, 390, 457-466. PubMed id: 19426740 DOI: 10.1016/j.jmb.2009.04.074

Date:

08-Sep-08 Release date: 30-Jun-09

Protein chains

Q8X123  (Q8X123_9AGAR) -  Agglutinin

Seq: 293 a.a.

Struc: 292 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

DOI no: 10.1016/j.jmb.2009.04.074

J Mol Biol 390:457-466 (2009)

PubMed id: 19426740

Structural Characterization of a Lectin from the Mushroom Marasmius oreades in Complex with the Blood Group B Trisaccharide and Calcium.

E.M.Grahn, H.C.Winter, H.Tateno, I.J.Goldstein, U.Krengel.

ABSTRACT

MOA, a lectin isolated from the fruiting bodies of the mushroom Marasmius oreades, specifically binds non-reducing terminal Galalpha(1,3)Gal-carbohydrates, such as occurs in the xenotransplantation epitope Galalpha(1,3)Galbeta(1,4)GlcNAc and the branched blood group B determinant Galalpha(1,3)[Fucalpha(1,2)]Gal. Here, we present the crystal structure of MOA in complex with the blood group B trisaccharide solved at 1.8 A resolution. To our knowledge, this is the first blood group B specific structure reported in complex with a blood group B determinant. The carbohydrate ligand binds to all three binding sites of the N-terminal beta-trefoil domain. Also, in this work Ca(2+) was included in the crystals, and binding of Ca(2+) to the MOA homodimer alters the conformation of the C-terminal domain by opening up the cleft containing a putative catalytic site.

Selected figure(s)

Figure 1.
Fig. 1. MOA in complex with the blood group B determinant. (a) Schematic representation of the MOA homodimer. One protomer is shown in green, and the other changes from blue at the N-terminus to red at the C-terminus. The four calcium ions bound as binuclear centers at the dimer interface are represented by dark blue spheres, and the bound blood group B trisaccharide molecules are represented as yellow stick models. (b) The surface of the γ-site is depicted together with the trisaccharide Galα(1,3)[Fucα(1,2)]Gal shown as a stick model. The final 2F[o] − F[c] electron density map (contoured at 1.0σ) is shown for the carbohydrate. The protein surface is shown in red for negative charges, in white for hydrophobic residues, in light blue for polar nitrogens, and in pink for polar oxygens. All figures were made using PyMoL (http://pymol.sourceforge.net/).

Figure 3.
Fig. 3. Conformational changes induced by the binding of calcium. (a) Superimposition of MOA C^α traces for the two ligand complexes. Only one protomer is shown for each MOA structure; however, all four calcium ions bound as two binuclear centers at the dimer interface are shown. The structure in complex with the xenotransplantation epitope Galα(1,3)Galβ(1,4)GlcNAc (no Ca^2+ bound) is shown in gray, and the complex with the blood group B trisaccharide Galα(1,3)[Fucα(1,2)]Gal (Ca^2+ bound) is shown from blue at the N-terminus to red at the C-terminus. Galα(1,3)Galβ(1,4)GlcNAc trisaccharides are drawn as gray stick models, and Galα(1,3)[Fucα(1,2)]Gal trisaccharides are shown as yellow stick models. Calcium ions are indicated by blue spheres. (b) Close-up view of a part of the protein (corresponding to residues 170–190) boxed in (a) to illustrate the movement of residues 182 and 183 upon calcium binding. (c) Stereo figure showing the details of calcium coordination at the dimer interface. Calcium ions are represented as blue spheres, and interacting protein residues are shown as stick models in green and blue for the two protomers, respectively. Calcium coordination is indicated by broken lines, and water molecules are depicted as red spheres.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 390, 457-466) copyright 2009.

Figures were selected by the author.