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PDBsum entry 2dty
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Sugar binding protein
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PDB id
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2dty
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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 carbohydrate-Specificity of basic winged-Bean lectin and its differential affinity for gal and galnac.
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Authors
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K.A.Kulkarni,
S.Katiyar,
A.Surolia,
M.Vijayan,
K.Suguna.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2006,
62,
1319-1324.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the complexes of basic winged-bean lectin with
galactose, 2-methoxygalactose, N-acetylgalactosamine and
methyl-alpha-N-acetylgalactosamine have been determined. Lectin-sugar
interactions involve four hydrogen bonds and a stacking interaction in all of
the complexes. In addition, an N-H...O hydrogen bond involving the hydroxyl
group at C2 exists in the galactose and 2-methoxygalactose complexes. An
additional hydrophobic interaction involving the methyl group in the latter
leads to the higher affinity of the methyl derivative. In the
lectin-N-acetylgalactosamine complex the N-H...O hydrogen bond is lost, but a
compensatory hydrogen bond is formed involving the O atom of the acetamido
group. In addition, the CH(3) moiety of the acetamido group is involved in
hydrophobic interactions. Consequently, the 2-methyl and acetamido derivatives
of galactose have nearly the same affinity for the lectin. The methyl group
alpha-linked to the galactose takes part in additional hydrophobic interactions.
Therefore, methyl-alpha-N-acetylgalactosamine has a higher affinity than
N-acetylgalactosamine for the lectin. The structures of basic winged-bean
lectin-sugar complexes provide a framework for examining the relative affinity
of galactose and galactosamine for the lectins that bind to them. The complexes
also lead to a structural explanation for the blood-group specificity of basic
winged-bean lectin.
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Figure 1.
Figure 1 Dimeric structure of WBAI complexed with galactose.
Ca^2+ and Mn^2+ are shown in spheres. Galactose and N-linked
glycans are shown in stick representation. This figure was
produced using PyMOL (http://www.pymol.org ).
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Figure 4.
Figure 4 Schematic representation of blood-group determinants.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2006,
62,
1319-1324)
copyright 2006.
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Secondary reference #1
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Title
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Carbohydrate specificity and quaternary association in basic winged bean lectin: X-Ray analysis of the lectin at 2.5 a resolution.
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Authors
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M.M.Prabu,
R.Sankaranarayanan,
K.D.Puri,
V.Sharma,
A.Surolia,
M.Vijayan,
K.Suguna.
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Ref.
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J Mol Biol, 1998,
276,
787-796.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1. The C^α trace of WBAI monomer. β-Sheets are
marked in black and the loops are in grey. The non-covalently
bound sugar and N-glycosylated sugars are in ball and stick
representation. The manganese ion (small) and the calcium ion
(big) are shown as hard spheres. This and the subsequent black
and white Figures were made using Molscript [Kraulis 1991].
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Figure 4.
Figure 4. N-glycosylation sites of WBAI (green circle) and
EcorL (red circle) shown on the canonical dimer.
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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Secondary reference #2
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Title
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Structural basis for the specificity of basic winged bean lectin for the tn-Antigen: a crystallographic, Thermodynamic and modelling study.
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Authors
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K.A.Kulkarni,
S.Sinha,
S.Katiyar,
A.Surolia,
M.Vijayan,
K.Suguna.
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Ref.
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FEBS Lett, 2005,
579,
6775-6780.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Dimeric structure of WBAI complexed with
Tn-antigen. Ca^2+ and Mn^2+ are shown in spheres. Tn-antigen and
N-linked glycans are shown in sticks. Figs. 2 and 3 were made
with the program MOLMOL [35].
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Figure 3.
Fig. 3. (A) WBAI–Tn-antigen hydrogen bonding
interactions. Four loops at the binding site are shown as coils
(B) A view, slightly different for the sake of clarity, from
that in (A) indicating the possible interactions involving the
modelled N-acetyl and N-methyl amide groups. Only hydrogen bonds
involving these groups are indicated. The other lectin–sugar
interactions remain the same as in (A).
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The above figures are
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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Secondary reference #3
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Title
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Structure of basic winged-Bean lectin and a comparison with its saccharide-Bound form.
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Authors
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N.Manoj,
V.R.Srinivas,
K.Suguna.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 1999,
55,
794-800.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2 The dimer of WBAI. The calcium and manganese ions are
shown as spheres. The carbohydrate-binding loops are coloured
black. This figure, Fig. 3-and Fig. 5-were generated using the
program MOLSCRIPT (Kraulis, 1991[Kraulis, P. J. (1991). J. Appl.
Cryst. 24, 946-950.]).
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Figure 7.
Figure 7 Stereoview showing the density of water molecules
located in the carbohydrate-binding region of the
saccharide-free form of WBAI. These water molecules occupy the
positions of O3, O4 and O6 of methyl-  -D-galactose
(thin lines) bound to WBAI in the complex.
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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