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PDBsum entry 1qdc
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protein ligands metals Protein-protein interface(s) links
Sugar binding protein PDB id
1qdc

 

 

 

 

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Contents
Protein chains
237 a.a. *
Ligands
MMA-MAN ×4
Metals
_CL
_CA ×4
_MN ×4
Waters ×386
* Residue conservation analysis
PDB id:
1qdc
Name: Sugar binding protein
Title: Man(aplha1-6)man(alpha1-o)methyl concanavalin a complex
Structure: Protein (concanavalin a). Chain: a, b, c, d. Synonym: con a. Other_details: co-crystals of concanavalin a with methyl-6--o-(alpha- d-mannopyranosyl)-alpha- d-mannopyranoside
Source: Canavalia ensiformis. Jack bean. Organism_taxid: 3823
Biol. unit: Tetramer (from PDB file)
Resolution:
2.00Å     R-factor:   0.175     R-free:   0.211
Authors: J.Bouckaert,R.Loris,L.Wyns
Key ref:
J.Bouckaert et al. (1999). The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A. J Biol Chem, 274, 29188-29195. PubMed id: 10506175 DOI: 10.1074/jbc.274.41.29188
Date:
14-Jul-98     Release date:   14-Oct-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P55915  (CONA_CANBR) -  Concanavalin-Br from Canavalia brasiliensis
Seq:
Struc: 		237 a.a.
237 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 

 
DOI no: 10.1074/jbc.274.41.29188 J Biol Chem 274:29188-29195 (1999)
PubMed id: 10506175  
 
 
The crystal structures of Man(alpha1-3)Man(alpha1-O)Me and Man(alpha1-6)Man(alpha1-O)Me in complex with concanavalin A.
J.Bouckaert, T.W.Hamelryck, L.Wyns, R.Loris.
 
  ABSTRACT  
 
The crystal structures of concanavalin A in complex with Man(alpha1-6)Man(alpha1-O)Me and Man(alpha1-3)Man(alpha1-O)Me were determined at resolutions of 2.0 and 2.8 A, respectively. In both structures, the O-1-linked mannose binds in the conserved monosaccharide-binding site. The O-3-linked mannose of Man(alpha1-3)Man(alpha1-O)Me binds in the hydrophobic subsite formed by Tyr-12, Tyr-100, and Leu-99. The shielding of a hydrophobic surface is consistent with the associated large heat capacity change. The O-6-linked mannose of Man(alpha1-6)Man(alpha1-O)Me binds in the same subsite formed by Tyr-12 and Asp-16 as the reducing mannose of the highly specific trimannose Man(alpha1-3)[Man(alpha1-6)]Man(alpha1-O)Me. However, it is much less tightly bound. Its O-2 hydroxyl makes no hydrogen bond with the conserved water 1. Water 1 is present in all the sugar-containing concanavalin A structures and increases the complementarity between the protein-binding surface and the sugar, but is not necessarily a hydrogen-bonding partner. A water analysis of the carbohydrate-binding site revealed a conserved water molecule replacing O-4 on the alpha1-3-linked arm of the trimannose. No such water is found for the reducing or O-6-linked mannose. Our data indicate that the central mannose of Man(alpha1-3)[Man(alpha1-6)]Man(alpha1-O)Me primarily functions as a hinge between the two outer subsites.
 
  Selected figure(s)  
 
Figure 4.
Fig. 4. Binding of Man( 1-3)Man( 1-O)Me in the hydrophobic subsite. a, superposition of M3M·ConA ( light gray) and 4'-methylumbelliferyl- -D-glucopyranoside (black). The O-3-linked mannose of M3M occupies the same subsite as the aglycon methylumbelliferyl of the substituted glucose. The conformations around the glycosidic linkages are similar. b, the hydrophobic character of the M3M subsite. M3M is shown as a ball-and-stick model. The van der Waals surface of ConA is colored according to residue properties: hydrophobic (brown), basic (blue), acidic (red), other polar residues (light green), or glycine (yellow). This figure was created using GRASP (49). 		Figure 5.
Fig. 5. Expulsion of water from the binding site of sugar-free ConA upon binding of M3M6M. Shown is a stereo figure of the superposition of waters 01-08 of sugar-free ConA on the M3M6M·ConA complex in the carbohydrate-binding site. This figure was created using BOBSCRIPT (48).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 29188-29195) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20458389 E.Mahon, T.Aastrup, and M.Barboiu (2010).
Multivalent recognition of lectins by glyconanoparticle systems.
  Chem Commun (Camb), 46, 5491-5493.  
19053475 R.Kadirvelraj, B.L.Foley, J.D.Dyekjaer, and R.J.Woods (2008).
Involvement of water in carbohydrate-protein binding: concanavalin A revisited.
  J Am Chem Soc, 130, 16933-16942.
PDB code: 3d4k
17683532 P.Delatorre, B.A.Rocha, E.P.Souza, T.M.Oliveira, G.A.Bezerra, F.B.Moreno, B.T.Freitas, T.Santi-Gadelha, A.H.Sampaio, W.F.Azevedo, and B.S.Cavada (2007).
Structure of a lectin from Canavalia gladiata seeds: new structural insights for old molecules.
  BMC Struct Biol, 7, 52.
PDB codes: 1wuv 2d7f
  17077488 F.B.Moreno, G.A.Bezerra, T.M.de Oliveira, E.P.de Souza, B.A.da Rocha, R.G.Benevides, P.Delatorre, B.S.Cavada, and W.F.de Azevedo (2006).
New crystal forms of Diocleinae lectins in the presence of different dimannosides.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 1100-1103.  
16704415 L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.J.Boons, S.Beeckmans, W.Versées, L.Wyns, and R.Loris (2006).
Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin.
  FEBS J, 273, 2407-2420.
PDB codes: 2ar6 2arb 2are 2arx 2auy
12010488 C.S.Hung, J.Bouckaert, D.Hung, J.Pinkner, C.Widberg, A.DeFusco, C.G.Auguste, R.Strouse, S.Langermann, G.Waksman, and S.J.Hultgren (2002).
Structural basis of tropism of Escherichia coli to the bladder during urinary tract infection.
  Mol Microbiol, 44, 903-915.
PDB codes: 1kiu 1klf
11509352 R.A.Bryce, I.H.Hillier, and J.H.Naismith (2001).
Carbohydrate-protein recognition: molecular dynamics simulations and free energy analysis of oligosaccharide binding to concanavalin A.
  Biophys J, 81, 1373-1388.  
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.

 

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