PDBsum entry 2vmc

Cell adhesion

PDB id: 2vmc

Contents

Protein chain

252 a.a. *

Ligands

A2G-NGA

1PG ×2

EDO

Metals

_CL ×2

_CA

Waters ×358

* Residue conservation analysis

PDB id:

2vmc

Name:

Cell adhesion

Title:

Structure of the complex of discoidin ii from dictyostelium discoideum with n-acetyl-galactosamine

Structure:

Discoidin-2. Chain: a. Synonym: discoidin ii. Engineered: yes. Other_details: galactose-binding domain 163-257

Source:

Dictyostelium discoideum. Slime mold. Organism_taxid: 366501. Strain: ax2. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: rosetta2 plyss.

Resolution:

1.90Å R-factor: 0.159 R-free: 0.198

Authors:

K.Saboia,M.Satre,A.Imberty,A.Varrot

Key ref:

K.S.Aragão et al. (2008). Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain. Proteins, 73, 43-52. PubMed id: 18384150

Date:

25-Jan-08 Release date: 01-Jul-08

Protein chain

P42530  (DIS2_DICDI) -  Discoidin-2 from Dictyostelium discoideum

Seq: 257 a.a.

Struc: 252 a.a.

Enzyme reactions

• Enzyme class: E.C.?

Proteins 73:43-52 (2008)

PubMed id: 18384150

Structure determination of Discoidin II from Dictyostelium discoideum and carbohydrate binding properties of the lectin domain.

K.S.Aragão, M.Satre, A.Imberty, A.Varrot.

ABSTRACT

The social amoeba Dictyostelium discoideum adopts a cohesive stage upon starvation and then produces Discoidin I and II, two proteins able to bind galactose and N-acetyl-galactosamine. The N-terminal domain or discoidin domain (DS) is widely distributed in eukaryotes where it plays a role in extracellular matrix binding while the C-terminal domain displays sequence similarities to invertebrate lectins. We present the first X-ray structures of the wild-type and recombinant Discoidin II in unliganded state and in complex with monosaccharides. The protein forms a homotrimer which presents two binding surfaces situated on the opposite boundaries of the structure. The binding sites of the N-terminal domain contain PEG molecules that could mimics binding of natural ligand. The C-terminal lectin domain interactions with N-acetyl-D-galactosamine and methyl-beta-galactoside are described. The carbohydrate binding sites are located at the interface between monomers. Specificity for galacto configuration can be rationalized since the axial O4 hydroxyl group is involved in several hydrogen bonds with protein side chains. Titration microcalorimetry allowed characterization of affinity and demonstrated the enthalpy-driven character of the interaction. Those results highlight the structural differentiation of the DS domain involved in many cell-adhesion processes from the lectin activity of Dictyostelium discoidins.