PDBsum entry 1en2

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Sugar binding protein PDB id
Jmol PyMol
Protein chain
91 a.a. *
Waters ×76
* Residue conservation analysis
PDB id:
Name: Sugar binding protein
Title: Uda tetrasaccharide complex. Crystal structure of urtica dio agglutinin, a superantigen presented by mhc molecules of cl class ii
Structure: Agglutinin isolectin i/agglutinin isolectin v/ ag isolectin vi. Chain: a. Synonym: uda. Other_details: three isoforms are present in the crystal: i i, v, and vi
Source: Urtica dioica. Great nettle. Organism_taxid: 3501. Other_details: purified from the rhizomes
1.40Å     R-factor:   0.198     R-free:   0.203
Authors: F.A.Saul,P.Rovira,G.Boulot,E.J.M.Van Damme,W.J.Peumans,P.Tru Bachi,G.A.Bentley
Key ref:
F.A.Saul et al. (2000). Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II. Structure, 8, 593-603. PubMed id: 10873861 DOI: 10.1016/S0969-2126(00)00142-8
20-Mar-00     Release date:   21-Jun-00    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P11218  (AGI_URTDI) -  Lectin/endochitinase 1
372 a.a.
91 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Chitinase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of the 1,4-beta-linkages of N-acetyl-D-glucosamine polymers of chitin.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     chitin binding     1 term  


DOI no: 10.1016/S0969-2126(00)00142-8 Structure 8:593-603 (2000)
PubMed id: 10873861  
Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
F.A.Saul, P.Rovira, G.Boulot, E.J.Damme, W.J.Peumans, P.Truffa-Bachi, G.A.Bentley.
BACKGROUND: Urtica dioica agglutinin (UDA), a monomeric lectin extracted from stinging nettle rhizomes, is specific for saccharides containing N-acetylglucosamine (GlcNAc). The lectin behaves as a superantigen for murine T cells, inducing the exclusive proliferation of Vbeta8.3(+) lymphocytes. UDA is unique among known T cell superantigens because it can be presented by major histocompatibility complex (MHC) molecules of both class I and II. RESULTS: The crystal structure of UDA has been determined in the ligand-free state, and in complex with tri-acetylchitotriose and tetra-acetylchitotetraose at 1.66 A, 1.90 A and 1.40 A resolution, respectively. UDA comprises two hevein-like domains, each with a saccharide-binding site. A serine and three aromatic residues at each site form the principal contacts with the ligand. The N-terminal domain binding site can centre on any residue of a chito-oligosaccharide, whereas that of the C-terminal domain is specific for residues at the nonreducing terminus of the ligand. We have shown previously that oligomers of GlcNAc inhibit the superantigenic activity of UDA and that the lectin binds to glycans on the MHC molecule. We show that UDA also binds to glycans on the T cell receptor (TCR). CONCLUSIONS: The presence of two saccharide-binding sites observed in the structure of UDA suggests that its superantigenic properties arise from the simultaneous fixation of glycans on the TCR and MHC molecules of the T cell and antigen-presenting cell, respectively. The well defined spacing between the two binding sites of UDA is probably a key factor in determining the specificity for Vbeta8.3(+) lymphocytes.
  Selected figure(s)  
Figure 5.
Figure 5. Stereoviews comparing the orientations of the tri- and tetrasaccharide ligands at binding sites A and B. (a) View of the molecular surface of site A showing the tri- and tetrasaccharide ligands in red and green, respectively. (b) View of the molecular surface of site B showing the tri- and tetrasaccharides in red and yellow, respectively. (c) Superposition of the a-carbon skeleton of domain A (red) onto domain B (white) for the tetrasaccharide complex. The ligand at site A is green and that at site B is yellow. This figure was created using VMD [61] and Raster-3D [60].
  The above figure is reprinted by permission from Cell Press: Structure (2000, 8, 593-603) copyright 2000.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20953796 S.Uslu, A.Bulbul, B.Diler, E.K.Bas, and A.Nuhoglu (2011).
Urticaria due to Urtica dioica in a neonate.
  Eur J Pediatr, 170, 401-403.  
  21500331 V.Roldós, F.J.Cañada, and J.Jiménez-Barbero (2011).
Carbohydrate-protein interactions: a 3D view by NMR.
  Chembiochem, 12, 990.  
20652910 J.J.Hernández-Gay, A.Ardá, S.Eller, S.Mezzato, B.R.Leeflang, C.Unverzagt, F.J.Cañada, and J.Jiménez-Barbero (2010).
Insights into the dynamics and molecular recognition features of glycopeptides by protein receptors: the 3D solution structure of hevein bound to the trisaccharide core of N-glycoproteins.
  Chemistry, 16, 10715-10726.  
20544965 Y.Kezuka, M.Kojima, R.Mizuno, K.Suzuki, T.Watanabe, and T.Nonaka (2010).
Structure of full-length class I chitinase from rice revealed by X-ray crystallography and small-angle X-ray scattering.
  Proteins, 78, 2295-2305.
PDB code: 3iwr
16183648 J.Balzarini, K.Van Laethem, S.Hatse, M.Froeyen, W.Peumans, E.Van Damme, and D.Schols (2005).
Carbohydrate-binding agents cause deletions of highly conserved glycosylation sites in HIV GP120: a new therapeutic concept to hit the achilles heel of HIV.
  J Biol Chem, 280, 41005-41014.  
16220560 M.I.Chávez, C.Andreu, P.Vidal, N.Aboitiz, F.Freire, P.Groves, J.L.Asensio, G.Asensio, M.Muraki, F.J.Cañada, and J.Jiménez-Barbero (2005).
On the importance of carbohydrate-aromatic interactions for the molecular recognition of oligosaccharides by proteins: NMR studies of the structure and binding affinity of AcAMP2-like peptides with non-natural naphthyl and fluoroaromatic residues.
  Chemistry, 11, 7060-7074.
PDB codes: 1znt 1zuv 1zwu
14675430 E.J.Van Damme, A.Barre, P.Rougé, and W.J.Peumans (2004).
Potato lectin: an updated model of a unique chimeric plant protein.
  Plant J, 37, 34-45.  
14769793 H.A.van den Burg, C.A.Spronk, S.Boeren, M.A.Kennedy, J.P.Vissers, G.W.Vuister, Wit, and J.Vervoort (2004).
Binding of the AVR4 elicitor of Cladosporium fulvum to chitotriose units is facilitated by positive allosteric protein-protein interactions: the chitin-binding site of AVR4 represents a novel binding site on the folding scaffold shared between the invertebrate and the plant chitin-binding domain.
  J Biol Chem, 279, 16786-16796.  
15368576 N.Aboitiz, M.Vila-Perelló, P.Groves, J.L.Asensio, D.Andreu, F.J.Cañada, and J.Jiménez-Barbero (2004).
NMR and modeling studies of protein-carbohydrate interactions: synthesis, three-dimensional structure, and recognition properties of a minimum hevein domain with binding affinity for chitooligosaccharides.
  Chembiochem, 5, 1245-1255.
PDB code: 1t0w
15039554 T.Fujii, M.Hayashida, M.Hamasu, M.Ishiguro, and Y.Hata (2004).
Structures of two lectins from the roots of pokeweed (Phytolacca americana).
  Acta Crystallogr D Biol Crystallogr, 60, 665-673.
PDB codes: 1uha 1uln
14962388 Y.Zhao, Z.Li, S.J.Drozd, Y.Guo, W.Mourad, and H.Li (2004).
Crystal structure of Mycoplasma arthritidis mitogen complexed with HLA-DR1 reveals a novel superantigen fold and a dimerized superantigen-MHC complex.
  Structure, 12, 277-288.
PDB code: 1r5i
12676931 H.Hemmi, J.Ishibashi, T.Tomie, and M.Yamakawa (2003).
Structural basis for new pattern of conserved amino acid residues related to chitin-binding in the antifungal peptide from the coconut rhinoceros beetle Oryctes rhinoceros.
  J Biol Chem, 278, 22820-22827.
PDB code: 1iyc
11786557 L.J.Olson, J.Zhang, N.M.Dahms, and J.J.Kim (2002).
Twists and turns of the cation-dependent mannose 6-phosphate receptor. Ligand-bound versus ligand-free receptor.
  J Biol Chem, 277, 10156-10161.
PDB code: 1keo
11679714 K.Harata, W.D.Schubert, and M.Muraki (2001).
Structure of Urtica dioica agglutinin isolectin I: dimer formation mediated by two zinc ions bound at the sugar-binding site.
  Acta Crystallogr D Biol Crystallogr, 57, 1513-1517.
PDB code: 1iqb
11173474 S.C.Ha, K.Min, J.C.Koo, Y.Kim, D.J.Yun, M.J.Cho, and K.K.Kim (2001).
Crystallization and preliminary crystallographic studies of an antimicrobial protein from Pharbitis nil.
  Acta Crystallogr D Biol Crystallogr, 57, 263-265.  
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.