Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 29442.12 
• Atom Count: 2033 
• Residue Count: 257 
• Unique protein chains: 1

2VMD

Structure of the complex of discoidin II from Dictyostelium discoideum with beta-methyl-galactose

• DOI: 10.2210/pdb2VMD/pdb

• Classification: CELL ADHESION
• Organism(s): Dictyostelium discoideum
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2008-01-25 Released: 2008-07-01 
• Deposition Author(s): Aragao, K.S., Satre, M., Imberty, A., Varrot, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.227 
• R-Value Work: 0.178 

Literature

Structure Determination of Discoidin II from Dictyostelium Discoideum and Carbohydrate Binding Properties of the Lectin Domain.

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

(2008) Proteins 73: 43

• PubMed: 18384150 
• DOI: 10.1002/prot.22038
• Primary Citation of Related Structures:  
  2VME, 2VMC, 2VM9


• PubMed 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.

---

Organizational Affiliation: 

CERMAV-CNRS (affiliated with University Joseph Fourier), Grenoble, France.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
DISCOIDIN-2	A	257	Dictyostelium discoideum	Mutation(s): 0  Gene Names: dscE
Find proteins for P42530 (Dictyostelium discoideum) Go to UniProtKB:  P42530

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
1PG	A	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL C11 H24 O6 SLNYBUIEAMRFSZ-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CA	A	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MBG	A	METHYL-BETA-GALACTOSE C7 H14 O6 HOVAGTYPODGVJG-VOQCIKJUSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
MBG	Kd: 950000 nM BINDINGMOAD
MBG	Kd: 950000 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.227 
• R-Value Work: 0.178 
• Space Group: H 3 2

Unit Cell:

Length (Å)	Angle (°)
a = 81.140	α = 90.00
b = 81.140	β = 90.00
c = 259.280	γ = 120.00

Software Package:

Software Name	Purpose
XDS	data reduction
SCALA	data scaling
REFMAC	refinement
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-25 
• Released Date: 2008-07-01 
• Deposition Author(s): Aragao, K.S., Satre, M., Imberty, A., Varrot, A.

Revision History 

• Version 1.0: 2008-07-01
  Type: Initial release
• Version 1.1: 2011-06-02
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance