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DOI no:
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Structure
8:593-603
(2000)
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PubMed id:
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Crystal structure of Urtica dioica agglutinin, a superantigen presented by MHC molecules of class I and class II.
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F.A.Saul,
P.Rovira,
G.Boulot,
E.J.Damme,
W.J.Peumans,
P.Truffa-Bachi,
G.A.Bentley.
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ABSTRACT
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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.
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Selected figure(s)
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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].
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The above figure is
reprinted
by permission from Cell Press:
Structure
(2000,
8,
593-603)
copyright 2000.
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Figure was
selected
by an automated process.
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Literature references that cite this PDB file's
key reference
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PubMed id
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Reference
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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.
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J Biol Chem, 280,
41005-41014.
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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.
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Chemistry, 11,
7060-7074.
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PDB codes:
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E.J.Van Damme,
A.Barre,
P.Rougé,
and
W.J.Peumans
(2004).
Potato lectin: an updated model of a unique chimeric plant protein.
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Plant J, 37,
34-45.
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H.A.van den Burg,
C.A.Spronk,
S.Boeren,
M.A.Kennedy,
J.P.Vissers,
G.W.Vuister,
P.J.de 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.
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J Biol Chem, 279,
16786-16796.
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T.Fujii,
M.Hayashida,
M.Hamasu,
M.Ishiguro,
and
Y.Hata
(2004).
Structures of two lectins from the roots of pokeweed (Phytolacca americana).
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Acta Crystallogr D Biol Crystallogr, 60,
665-673.
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PDB codes:
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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.
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J Biol Chem, 278,
22820-22827.
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PDB code:
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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.
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J Biol Chem, 277,
10156-10161.
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PDB code:
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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.
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Acta Crystallogr D Biol Crystallogr, 57,
1513-1517.
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PDB code:
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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.
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Acta Crystallogr D Biol Crystallogr, 57,
263-265.
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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
codes are
shown on the right.
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91 a.a.
