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PDBsum entry 2d6p
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Sugar binding protein
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PDB id
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2d6p
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References listed in PDB file
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Key reference
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Title
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Crystal structure of the galectin-9 n-Terminal carbohydrate recognition domain from mus musculus reveals the basic mechanism of carbohydrate recognition.
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Authors
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M.Nagae,
N.Nishi,
T.Murata,
T.Usui,
T.Nakamura,
S.Wakatsuki,
R.Kato.
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Ref.
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J Biol Chem, 2006,
281,
35884-35893.
[DOI no: ]
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PubMed id
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Abstract
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The galectins are a family of beta-galactoside-binding animal lectins with a
conserved carbohydrate recognition domain (CRD). They have a high affinity for
small beta-galactosides, but binding specificity for complex glycoconjugates
varies considerably within the family. The ligand recognition is essential for
their proper function, and the structures of several galectins have suggested
their mechanism of carbohydrate binding. Galectin-9 has two tandem CRDs with a
short linker, and we report the crystal structures of mouse galectin-9
N-terminal CRD (NCRD) in the absence and the presence of four ligand complexes.
All structures form the same dimer, which is quite different from the canonical
2-fold symmetric dimer seen for galectin-1 and -2. The beta-galactoside
recognition mechanism in the galectin-9 NCRD is highly conserved among other
galectins. In the apo form structure, water molecules mimic the ligand
hydrogen-bond network. The galectin-9 NCRD can bind both N-acetyllactosamine
(Galbeta1-4GlcNAc) and T-antigen (Galbeta1-3GalNAc) with the proper location of
Arg-64. Moreover, the structure of the N-acetyllactosamine dimer
(Galbeta1-4GlcNAcbeta1-3Galbeta1-4GlcNAc) complex shows a unique binding mode of
galectin-9. Finally, surface plasmon resonance assay showed that the galectin-9
NCRD forms a homophilic dimer not only in the crystal but also in solution.
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Figure 1.
FIGURE 1. Crystal structure of the mouse galectin-9
N-terminal CRD. A, ribbon model of the monomeric structure of
the apo form1 of the galectin-9 N-terminal CRD is shown. The
five-stranded (F1–F5) and six-stranded (S1–S6)  -sheets
and one short helix (H1) are indicated by the letter-number
code. The carbohydrate binding site is shown by a dotted box. B,
the dimeric structure of the galectin-9 N-terminal CRD is shown.
Two monomers in an asymmetric unit in the apo form1 crystal are
shown in red (chain-A) and green (chain-B), respectively. C,
close up view of the dimer interface. The amino acid residues
involved in the dimer formation are shown in ball-and-stick
model. The carbon, oxygen, nitrogen, and sulfur atoms are shown
in white, red, blue, and yellow spheres, respectively. Hydrogen
bonds are depicted by red dotted lines. D, electrostatic
potential maps of the dimer surfaces of the galectin-9
N-terminal CRD (upper) and galectin-1 CRD (lower) (PDB code:
1GZW). Positive (blue) and negative (red) potentials are mapped
on the van der Waals surfaces in the range –10 k[B]T (red) to
+10 k[B]T (blue), where k[B] is Boltzmann's constant and T is
the absolute temperature. The orientation of the galectin-9
N-terminal CRD dimer is same as Fig. 1B.
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Figure 4.
FIGURE 4. Crystal structure of the galectin-9 N-terminal
CRD-LN2 complex. A, the galectin-9 N-terminal CRD dimer and LN2
molecule are represented by ribbon model and rod model with
2F[o] – F[c] map contoured at 1  , respectively. B, the
electrostatic potential of the protein dimer in the complex is
mapped to the molecular surface of the protein as in Fig. 1D.
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The above figures are
reprinted
by permission from the ASBMB:
J Biol Chem
(2006,
281,
35884-35893)
copyright 2006.
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