PDBsum entry 2vmc

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protein ligands metals links
Cell adhesion PDB id
Protein chain
252 a.a. *
1PG ×2
_CL ×2
Waters ×358
* Residue conservation analysis
PDB id:
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.
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
25-Jan-08     Release date:   01-Jul-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P42530  (DIS2_DICDI) -  Discoidin-2
257 a.a.
252 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     vesicle   3 terms 
  Biological process     macropinocytosis   4 terms 
  Biochemical function     carbohydrate binding     5 terms  


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.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
21356102 R.Sucgang, A.Kuo, X.Tian, W.Salerno, A.Parikh, C.L.Feasley, E.Dalin, H.Tu, E.Huang, K.Barry, E.Lindquist, H.Shapiro, D.Bruce, J.Schmutz, A.Salamov, P.Fey, P.Gaudet, C.Anjard, M.M.Babu, S.Basu, Y.Bushmanova, H.van der Wel, M.Katoh-Kurasawa, C.Dinh, P.M.Coutinho, T.Saito, M.Elias, P.Schaap, R.R.Kay, B.Henrissat, L.Eichinger, F.Rivero, N.H.Putnam, C.M.West, W.F.Loomis, R.L.Chisholm, G.Shaulsky, J.E.Strassmann, D.C.Queller, A.Kuspa, and I.V.Grigoriev (2011).
Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum.
  Genome Biol, 12, R20.  
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