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PDBsum entry 1jyi

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protein metals Protein-protein interface(s) links
Sugar binding protein PDB id
1jyi
Jmol
Contents
Protein chains
237 a.a. *
12 a.a. *
Metals
_CA ×4
_MN ×4
Waters ×289
* Residue conservation analysis
PDB id:
1jyi
Name: Sugar binding protein
Title: Concanavalin a/12-mer peptide complex
Structure: Concanavalin a. Chain: a, b, c, d. 12-mer peptide. Chain: p, q, r, s. Engineered: yes
Source: Canavalia ensiformis. Jack bean. Organism_taxid: 3823. Synthetic: yes. Other_details: the peptide was chemically synthesized.
Biol. unit: Octamer (from PDB file)
Resolution:
2.75Å     R-factor:   0.192     R-free:   0.265
Authors: D.Jain,K.J.Kaur,B.Sundaravadivel,D.M.Salunke
Key ref:
D.Jain et al. (2000). Structural and functional consequences of peptide-carbohydrate mimicry. Crystal structure of a carbohydrate-mimicking peptide bound to concanavalin A. J Biol Chem, 275, 16098-16102. PubMed id: 10821862 DOI: 10.1074/jbc.275.21.16098
Date:
12-Sep-01     Release date:   12-Sep-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P02866  (CONA_CANEN) -  Concanavalin-A
Seq:
Struc:
290 a.a.
237 a.a.*
Protein chains
No UniProt id for this chain
Struc: 12 a.a.
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 26 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     carbohydrate binding     1 term  

 

 
DOI no: 10.1074/jbc.275.21.16098 J Biol Chem 275:16098-16102 (2000)
PubMed id: 10821862  
 
 
Structural and functional consequences of peptide-carbohydrate mimicry. Crystal structure of a carbohydrate-mimicking peptide bound to concanavalin A.
D.Jain, K.Kaur, B.Sundaravadivel, D.M.Salunke.
 
  ABSTRACT  
 
The functional consequences of peptide-carbohydrate mimicry were analyzed on the basis of the crystal structure of concanavalin A (ConA) in complex with a carbohydrate-mimicking peptide, DVFYPYPYASGS. The peptide binds to the non-crystallographically related monomers of two independent dimers of ConA in two different modes, in slightly different conformations, demonstrating structural adaptability in ConA-peptide recognition. In one mode, the peptide has maximum interactions with ConA, and in the other, it shows relatively fewer contacts within this site but significant contacts with the symmetry-related subunit. Neither of the peptide binding sites overlaps with the structurally characterized mannose and trimannose binding sites on ConA. Despite this, the functional mimicry between the peptide and carbohydrate ligands was evident. The peptide-inhibited ConA induced T cell proliferation in a dose-dependent manner. The effect of the designed analogs of the peptide on ConA-induced T cell proliferation and their recognition by the antibody response against alpha-d-mannopyranoside indicate a role for aromatic residues in functional mimicry. Although the functional mimicry was observed between the peptide and carbohydrate moieties, the crystal structure of the ConA-peptide complex revealed that the two peptide binding sites are independent of the methyl alpha-d-mannopyranoside binding site.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Stereoview of the F[o] F[c] difference electron density map representing the peptide in P2 mode in ConA-12-mer complex.
Figure 4.
Fig. 4. Stereoview of the surface representation of the A subunit of ConA showing the bound peptide in the primary peptide binding site (PPBS) and the symmetry-related peptide in the secondary peptide binding site (SPBS). Comparison of the two sites has been made with respect to the trisaccharide binding site (TSBS) on ConA. The peptide molecules at the primary site (orange) and at the secondary site (pink) and trimannose (blue) are shown as stick drawings.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 16098-16102) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20156098 L.L.Eggink, M.Salas, C.V.Hanson, and J.K.Hoober (2010).
Peptide sugar mimetics prevent HIV type 1 replication in peripheral blood mononuclear cells in the presence of HIV-positive antiserum.
  AIDS Res Hum Retroviruses, 26, 149-160.  
19296440 B.Taneja, J.Yadav, T.K.Chakraborty, and S.K.Brahmachari (2009).
An Indian effort towards affordable drugs: "generic to designer drugs".
  Biotechnol J, 4, 348-360.  
19496993 G.Pandey, T.Fatma, and S.S.Komath (2009).
Specific interaction of the legume lectins, concanavalin a and peanut agglutinin, with phycocyanin.
  Photochem Photobiol, 85, 1126-1133.  
18198210 A.Menendez, D.A.Calarese, R.L.Stanfield, K.C.Chow, C.N.Scanlan, R.Kunert, H.Katinger, D.R.Burton, I.A.Wilson, and J.K.Scott (2008).
A peptide inhibitor of HIV-1 neutralizing antibody 2G12 is not a structural mimic of the natural carbohydrate epitope on gp120.
  FASEB J, 22, 1380-1392.
PDB code: 2oqj
18049865 B.H.Fasciotto, U.Kühn, D.V.Cohn, and S.U.Gorr (2008).
Secretory cargo composition affects polarized secretion in MDCK epithelial cells.
  Mol Cell Biochem, 310, 67-75.  
18032557 L.Krishnan, G.Sahni, K.J.Kaur, and D.M.Salunke (2008).
Role of antibody paratope conformational flexibility in the manifestation of molecular mimicry.
  Biophys J, 94, 1367-1376.
PDB code: 2v7h
17510954 K.A.Kulkarni, S.Katiyar, A.Surolia, M.Vijayan, and K.Suguna (2007).
Generation of blood group specificity: new insights from structural studies on the complexes of A- and B-reactive saccharides with basic winged bean agglutinin.
  Proteins, 68, 762-769.
PDB codes: 2e51 2e53 2e7q 2e7t
16525538 S.S.Komath, M.Kavitha, and M.J.Swamy (2006).
Beyond carbohydrate binding: new directions in plant lectin research.
  Org Biomol Chem, 4, 973-988.  
15998318 D.G.Robinson, P.Oliviusson, and G.Hinz (2005).
Protein sorting to the storage vacuoles of plants: a critical appraisal.
  Traffic, 6, 615-625.  
15159564 F.J.López-Jaramillo, L.A.González-Ramírez, A.Albert, F.Santoyo-González, A.Vargas-Berenguel, and F.Otálora (2004).
Structure of concanavalin A at pH 8: bound solvent and crystal contacts.
  Acta Crystallogr D Biol Crystallogr, 60, 1048-1056.
PDB code: 1nxd
14747704 M.Goel, P.Anuradha, K.J.Kaur, B.G.Maiya, M.J.Swamy, and D.M.Salunke (2004).
Porphyrin binding to jacalin is facilitated by the inherent plasticity of the carbohydrate-binding site: novel mode of lectin-ligand interaction.
  Acta Crystallogr D Biol Crystallogr, 60, 281-288.
PDB code: 1pxd
11943376 B.Monzavi-Karbassi, G.Cunto-Amesty, P.Luo, and T.Kieber-Emmons (2002).
Peptide mimotopes as surrogate antigens of carbohydrates in vaccine discovery.
  Trends Biotechnol, 20, 207-214.  
12472892 M.Simon-Haldi, N.Mantei, J.Franke, H.Voshol, and M.Schachner (2002).
Identification of a peptide mimic of the L2/HNK-1 carbohydrate epitope.
  J Neurochem, 83, 1380-1388.  
11371463 D.Jain, K.J.Kaur, and D.M.Salunke (2001).
Plasticity in protein-peptide recognition: crystal structures of two different peptides bound to concanavalin A.
  Biophys J, 80, 2912-2921.
PDB codes: 1jui 1jyc
11284160 H.J.Gabius (2001).
Glycohistochemistry: the why and how of detection and localization of endogenous lectins.
  Anat Histol Embryol, 30, 3.  
11288176 R.Ravishankar, C.J.Thomas, K.Suguna, A.Surolia, and M.Vijayan (2001).
Crystal structures of the peanut lectin-lactose complex at acidic pH: retention of unusual quaternary structure, empty and carbohydrate bound combining sites, molecular mimicry and crystal packing directed by interactions at the combining site.
  Proteins, 43, 260-270.
PDB codes: 1cq9 1cr7
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.