PDBsum entry 2wn3

Cell adhesion

PDB id: 2wn3

Contents

Protein chains

254 a.a. *

Ligands

GAL-NGA ×3

SO4 ×3

1PG

GOL ×3

Metals

_CA ×3

Waters ×1121

* Residue conservation analysis

PDB id:

2wn3

Name:

Cell adhesion

Title:

Crystal structure of discoidin i from dictyostelium discoideum in complex with the disaccharide galnac beta 1-3 galactose, at 1.6 a resolution.

Structure:

Discoidin-1 subunit a. Chain: a, b, c. Synonym: discoidin-1 subunit alpha, discoidin i chain a. Engineered: yes

Source:

Dictyostelium discoideum. Slime mold. Organism_taxid: 366501. Strain: ax2. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.59Å R-factor: 0.153 R-free: 0.180

Authors:

S.Mathieu,A.Imberty,A.Varrot

Key ref:

S.V.Mathieu et al. (2010). Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II. J Mol Biol, 400, 540-554. PubMed id: 20580724

Date:

07-Jul-09 Release date: 26-May-10

Protein chains

P02886  (DIS1A_DICDI) -  Discoidin-1 subunit A from Dictyostelium discoideum

Seq: 253 a.a.

Struc: 254 a.a.

J Mol Biol 400:540-554 (2010)

PubMed id: 20580724

Discoidin I from Dictyostelium discoideum and Interactions with oligosaccharides: specificity, affinity, crystal structures, and comparison with discoidin II.

S.V.Mathieu, K.S.Aragão, A.Imberty, A.Varrot.

ABSTRACT

Discoidin I and Discoidin II (DiscI and DiscII), are N-acetylgalactosamine-binding proteins from Dictyostelium discoideum. They consist of two domains with an N-terminal discoidin domain and a C-terminal H-type lectin domain. They were cloned and expressed in high yield in recombinant form in Escherichia coli. Although both lectins bind galactose and N-acetylgalactosamine, glycan array experiments performed on the recombinant proteins displayed strong differences in their specificity for oligosaccharides. DiscI and DiscII bind preferentially to Gal/GalNAcbeta1-3Gal/GalNAc-and Gal/GalNAcbeta1-4GlcNAcbeta1-6Gal/GalNAc-containing glycans respectively. The affinity of the interaction of DiscI with monosaccharides and disaccharides was evaluated using isothermal calorimetry experiments. The tree-dimensional structures of native DiscI and its complexes with GalNAc, GalNAcbeta1-3Gal and Galbeta1-3GalNAc were solved by X-ray crystallography. DiscI forms trimers with involvement of calcium at the monomer interface. The N-terminal discoidin domain presents structural similarity to F-type lectins such as the eel agglutinin where an amphiphilic binding pocket suggests a possible carbohydrate-binding activity. In the C-terminal H-type lectin domain, the GalNAc residue establishes specific hydrogen bonds that explain the observed affinity (K(d)= 3 10(-4) M). The different specificities of DiscI and DiscII for oligosaccharides were rationalized from the different structures obtained by either X-ray crystallography or molecular modelling.