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PDBsum entry 3ca5
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Sugar binding protein, plant protein
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PDB id
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3ca5
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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 sugar recognition, Including the tn carcinoma antigen, By the lectin sna-Ii from sambucus nigra.
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Authors
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L.Maveyraud,
H.Niwa,
V.Guillet,
D.I.Svergun,
P.V.Konarev,
R.A.Palmer,
W.J.Peumans,
P.Rougé,
E.J.Van damme,
C.D.Reynolds,
L.Mourey.
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Ref.
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Proteins, 2008,
75,
89.
[DOI no: ]
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PubMed id
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Abstract
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Bark of elderberry (Sambucus nigra) contains a galactose
(Gal)/N-acetylgalactosamine (GalNAc)-specific lectin (SNA-II) corresponding to
slightly truncated B-chains of a genuine Type-II ribosome-inactivating protein
(Type-II RIPs, SNA-V), found in the same species. The three-dimensional X-ray
structure of SNA-II has been determined in two distinct crystal forms, hexagonal
and tetragonal, at 1.90 A and 1.35 A, respectively. In both crystal forms, the
SNA-II molecule folds into two linked betabeta-trefoil domains, with an overall
conformation similar to that of the B-chains of ricin and other Type-II RIPs.
Glycosylation is observed at four sites along the polypeptide chain, accounting
for 14 saccharide units. The high-resolution structures of SNA-II in complex
with Gal and five Gal-related saccharides (GalNAc, lactose,
alphaalpha1-methylgalactose, fucose, and the carcinoma-specific Tn antigen) were
determined at 1.55 A resolution or better. Binding is observed in two
saccharide-binding sites for most of the sugars: a conserved aspartate residue
interacts simultaneously with the O3 and O4 atoms of saccharides. In one of the
binding sites, additional interactions with the protein involve the O6 atom.
Analytical gel filtration, small angle X-ray scattering studies and crystal
packing analysis indicate that, although some oligomeric species are present,
the monomeric species predominate in solution. Proteins 2009. (c) 2008
Wiley-Liss, Inc.
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Figure 1.
Figure 1. Ribbon representation of the structure of SNA-II. (a)
Stereoview of the overall structure of SNA-II colored from blue
(N terminus) to red (C terminus) as observed in the hexagonal
crystal form. The four glycosylation sites are labeled, and the
glycans are represented as pink sticks. Disulphide bridges are
represented as sticks. (b) View of Domains I (top) and II
(bottom) in two orthogonal orientations. In each domain,
subdomains  are
colored in red,  in
green, and  in
blue. The first and fourth -strands
of each subdomain forming the central -barrel
are indicated with vivid colors. Glycosylation sites and
saccharide-binding residues are labeled and represented as
sticks. Glycans are represented as pink sticks.
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Figure 4.
Figure 4. X-ray analysis of saccharide binding to SNA-II. (a)
Stereoview of the saccharide-binding sites of Domain I (top) and
of Domain II (bottom), with bound galactose (pink).
Saccharide-binding residues are labeled, and water molecules are
indicated with a red sphere. Hydrogen bonds are represented with
dotted lines. (b) Comparison of the binding of the different
saccharides used in this study (pink), except galactose, in the
saccharide-binding site of Domain I. The orientation is
identical as in (a).
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The above figures are
reprinted
by permission from John Wiley & Sons, Inc.:
Proteins
(2008,
75,
89)
copyright 2008.
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