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PDBsum entry 1ulm
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Sugar binding protein
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PDB id
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1ulm
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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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Similarity between protein-Protein and protein-Carbohydrate interactions, Revealed by two crystal structures of lectins from the roots of pokeweed.
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Authors
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M.Hayashida,
T.Fujii,
M.Hamasu,
M.Ishiguro,
Y.Hata.
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Ref.
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J Mol Biol, 2003,
334,
551-565.
[DOI no: ]
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PubMed id
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Abstract
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The roots of pokeweed (Phytolacca americana) are known to contain the lectins
designated PL-A, PL-B, PL-C, PL-D1, and PL-D2. Of these lectins, the crystal
structures of two PLs, the ligand-free PL-C and the complex of PL-D2 with
tri-N-acetylchitotriose, have been determined at 1.8A resolution. The
polypeptide chains of PL-C and PL-D2 form three and two repetitive
chitin-binding domains, respectively. In the crystal structure of the PL-D2
complex, one trisaccharide molecule is shared mainly between two neighboring
molecules related to each other by a crystallographic 2(1)-screw axis, and
infinite helical chains of complexed molecules are generated by the sharing of
ligand molecules. The crystal structure of PL-C reveals that the molecule is a
dimer of two identical subunits, whose polypeptide chains are located in a
head-to-tail fashion by a molecular 2-fold axis. Three putative
carbohydrate-binding sites in each subunit are located in the dimer interface.
The dimerization of PL-C is performed through the hydrophobic interactions
between the carbohydrate-binding sites of the opposite domains in the dimer,
leading to a distinct dimerization mode from that of wheat-germ agglutinin.
Three aromatic residues in each carbohydrate-binding site of PL-C are involved
in the dimerization. These residues correspond to the residues that interact
mainly with the trisaccharide in the PL-D2 complex and appear to mimic the
saccharide residues in the complex. Consequently, the present structure of the
PL-C dimer has no room for accommodating carbohydrate. The quaternary structure
of PL-C formed through these putative carbohydrate-binding residues may lead to
the lack of hemagglutinating activity.
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Figure 4.
Figure 4. Binding mode of PL-D2 to tri-N-acetylchitotriose
in the crystal of the PL-D2 complex. Parts of three PL-D2
molecules binding a tri-N-acetylchitotriose molecule (yellow)
are shown: two independent molecules (A, sky-blue; B, green) in
the asymmetric unit, and A' (pink), in the next asymmetric unit,
which is related to A by a crystallographic 2[1]-screw axis. The
tri-N-acetylchitotriose molecule is shared mainly between domain
I of molecule A' and domain II of molecule A, and interacts with
Ser9 of molecule B.
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Figure 5.
Figure 5. Stereo view showing superposition of C^a traces
of chitin-binding domains. PL-C, the uncomplexed PL-D2 (PDB code
1UHA), the complexed PL-D2, UDA6 (PDB code 1EHH), and WGA1 (PDB
code 2CWG) are shown in blue, cyan, red, purple, and green,
respectively. All domains in each protein are shown in the same
color. Four disulfide bridges and three carbohydrate-binding
aromatic residues in each domain are shown by yellow sticks and
ball-and-sticks, respectively.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(2003,
334,
551-565)
copyright 2003.
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