PDBsum entry 2d6p

Sugar binding protein

PDB id: 2d6p

Contents

Protein chains

144 a.a. *

Ligands

NGA-GAL ×2

Waters ×58

* Residue conservation analysis

PDB id:

2d6p

Name:

Sugar binding protein

Title:

Crystal structure of mouse galectin-9 n-terminal crd in complex with t-antigen

Structure:

Lectin, galactose binding, soluble 9. Chain: a, b. Fragment: n-terminal carbohydrate recognition domain(residues 1-157). Synonym: galectin-9. Engineered: yes

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

2.70Å R-factor: 0.240 R-free: 0.296

Authors:

M.Nagae,N.Nishi,T.Nakamura,T.Murata,S.Wakatsuki,R.Kato

Key ref:

M.Nagae et al. (2006). Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition. J Biol Chem, 281, 35884-35893. PubMed id: 16990264 DOI: 10.1074/jbc.M606648200

Date:

14-Nov-05 Release date: 26-Sep-06

Protein chains

O08573  (LEG9_MOUSE) -  Galectin-9 from Mus musculus

Seq: 353 a.a.

Struc: 144 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M606648200

J Biol Chem 281:35884-35893 (2006)

PubMed id: 16990264

Crystal structure of the galectin-9 N-terminal carbohydrate recognition domain from Mus musculus reveals the basic mechanism of carbohydrate recognition.

M.Nagae, N.Nishi, T.Murata, T.Usui, T.Nakamura, S.Wakatsuki, R.Kato.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2006, 281, 35884-35893) copyright 2006.

Figures were selected by the author.