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PDBsum entry 2ar6
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Sugar binding protein
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PDB id
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2ar6
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References listed in PDB file
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Key reference
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Title
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Structural basis for the recognition of complex-Type biantennary oligosaccharides by pterocarpus angolensis lectin.
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Authors
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L.Buts,
A.Garcia-Pino,
A.Imberty,
N.Amiot,
G.J.Boons,
S.Beeckmans,
W.Versées,
L.Wyns,
R.Loris.
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Ref.
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FEBS J, 2006,
273,
2407-2420.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of Pterocarpus angolensis lectin is determined in its
ligand-free state, in complex with the fucosylated biantennary complex type
decasaccharide NA2F, and in complex with a series of smaller oligosaccharide
constituents of NA2F. These results together with thermodynamic binding data
indicate that the complete oligosaccharide binding site of the lectin consists
of five subsites allowing the specific recognition of the pentasaccharide GlcNAc
beta(1-2)Man alpha(1-3)[GlcNAc beta(1-2)Man alpha(1-6)]Man. The mannose on the
1-6 arm occupies the monosaccharide binding site while the GlcNAc residue on
this arm occupies a subsite that is almost identical to that of concanavalin A
(con A). The core mannose and the GlcNAc beta(1-2)Man moiety on the 1-3 arm on
the other hand occupy a series of subsites distinct from those of con A.
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Figure 2.
Fig. 2. The monosaccharide binding site of PAL. (A) Stereo
view of the monosaccharide binding site of PAL in absence of
bound carbohydrate. The electron density for four water
molecules that occupy the binding site is shown, together with
the hydrogen bond network these waters make with the protein.
Superimposed in black are the equivalent residues of the mannose
complex (subunit B in the asymmetric unit). The water molecules
clearly mimic the oxygen atoms of bound mannose (black, thick
lines). (B) Stereo view of the interactions of mannose in the
monosaccharide binding site. The beta-anomeric oxygen position
of mannose is drawn in light green, as is the corresponding
orientation of the side chain of Glu221. The second conformation
of the side chain of Glu221, which also adopts two conformations
but not correlated with the anomeric form of the bound mannose
is shown in dark green.
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Figure 8.
Fig. 8. Comparison between PAL and con A. (A) Comparison
between con A and PAL. Stereo view of the binding of M592
(green) to the –1 and M subsites of con A (colored according
to atom type). The corresponding situation in PAL is
superimposed as shown in thin black lines. (B) Downstream
binding sites. Stereo view of the binding of M592 (green) to the
+1, +2 and +3 subsites of con A (colored according to atom
type). The corresponding situation in PAL is superimposed as
shown in thin black lines.
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The above figures are
reprinted
by permission from the Federation of European Biochemical Societies:
FEBS J
(2006,
273,
2407-2420)
copyright 2006.
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