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PDBsum entry 1qdc
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Sugar binding protein
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PDB id
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1qdc
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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The crystal structures of man(alpha1-3)man(alpha1-O)me and man(alpha1-6)man(alpha1-O)me in complex with concanavalin a.
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Authors
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J.Bouckaert,
T.W.Hamelryck,
L.Wyns,
R.Loris.
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Ref.
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J Biol Chem, 1999,
274,
29188-29195.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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).
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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).
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(1999,
274,
29188-29195)
copyright 1999.
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Secondary reference #1
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Title
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A structure of the complex between concanavalin a and methyl-3,6-Di-O-(Alpha-D-Mannopyranosyl)-Alpha-D-Mannopyranoside reveals two binding modes.
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Authors
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R.Loris,
D.Maes,
F.Poortmans,
L.Wyns,
J.Bouckaert.
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Ref.
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J Biol Chem, 1996,
271,
30614-30618.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. Atom numbering scheme for the trimannose molecule.
The 1-6-linked
mannose is labeled as A, the core methyl- -D-mannose^
as B, and the 1-3-linked
mannose as C. The glycosidic torsion angles  ,  , and  are also
indicated. [a] =  (O5A-C1A-O1A-C6B),
[a] = (C1A-O1A-C6B-C5B),
and [a] = (O1A-C6B-C5B-O5B),
[c] (O5C-C1C-O1C-C3B),
and [c] = (C1C-O1C-C3B-C4B).
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Figure 3.
Fig. 3. Superpositions of the concanavalin
A-methyl-3,6-di-O-( -D-mannopyranosyl)-
-D-mannopyranoside
complex (black), the concanavalin A-methyl- -D-mannopyranoside
(gray) (Protein Data Base entry 5CNA) and saccharide-free
concanavalin A (PDB entry 1CON).
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The above figures are
reproduced from the cited reference
with permission from the ASBMB
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Secondary reference #2
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Title
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Structural basis of trimannoside recognition by concanavalin a.
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Authors
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J.H.Naismith,
R.A.Field.
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Ref.
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J Biol Chem, 1996,
271,
972-976.
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PubMed id
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Secondary reference #3
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Title
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Thermodynamics of lectin-Carbohydrate interactions. Titration microcalorimetry measurements of the binding of n-Linked carbohydrates and ovalbumin to concanavalin a.
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Authors
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D.K.Mandal,
N.Kishore,
C.F.Brewer.
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Ref.
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Biochemistry, 1994,
33,
1149-1156.
[DOI no: ]
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PubMed id
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