PDBsum entry 2ar6

Sugar binding protein

PDB id: 2ar6

Contents

Protein chains

240 a.a. *

Ligands

MAN-NAG

MAN-MAN-NAG-MAN-NAG

Metals

_CA ×2

_MN ×2

Waters ×303

* Residue conservation analysis

PDB id:

2ar6

Name:

Sugar binding protein

Title:

Pterocarpus angolensis lectin (pal) in complex with the pentasaccharide m592

Structure:

Lectin. Chain: a, b. Synonym: pal

Source:

Pterocarpus angolensis. Organism_taxid: 182271. Tissue: seed

Biol. unit:

Dimer (from PQS)

Resolution:

1.80Å R-factor: 0.176 R-free: 0.201

Authors:

L.Buts,A.Garcia-Pino,A.Imberty,N.Amiot,G.J.Boons,S.Beeckmans, W.Versees,L.Wyns,R.Loris

Key ref:

L.Buts et al. (2006). Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin. FEBS J, 273, 2407-2420. PubMed id: 16704415 DOI: 10.1111/j.1742-4658.2006.05248.x

Date:

19-Aug-05 Release date: 01-Aug-06

Protein chains

Q8GSD2  (Q8GSD2_PTEAG) -  Lectin (Fragment) from Pterocarpus angolensis

Seq: 260 a.a.

Struc: 240 a.a.

DOI no: 10.1111/j.1742-4658.2006.05248.x

FEBS J 273:2407-2420 (2006)

PubMed id: 16704415

Structural basis for the recognition of complex-type biantennary oligosaccharides by Pterocarpus angolensis lectin.

L.Buts, A.Garcia-Pino, A.Imberty, N.Amiot, G.J.Boons, S.Beeckmans, W.Versées, L.Wyns, R.Loris.

ABSTRACT

The crystal structure of Pterocarpus angolensis lectin is determined in its ligand-free state, in complex with the fucosylated biantennary complex type decasaccharide NA2F, and in complex with a series of smaller oligosaccharide constituents of NA2F. These results together with thermodynamic binding data indicate that the complete oligosaccharide binding site of the lectin consists of five subsites allowing the specific recognition of the pentasaccharide GlcNAc beta(1-2)Man alpha(1-3)[GlcNAc beta(1-2)Man alpha(1-6)]Man. The mannose on the 1-6 arm occupies the monosaccharide binding site while the GlcNAc residue on this arm occupies a subsite that is almost identical to that of concanavalin A (con A). The core mannose and the GlcNAc beta(1-2)Man moiety on the 1-3 arm on the other hand occupy a series of subsites distinct from those of con A.

Selected figure(s)

Figure 2.
Fig. 2. The monosaccharide binding site of PAL. (A) Stereo view of the monosaccharide binding site of PAL in absence of bound carbohydrate. The electron density for four water molecules that occupy the binding site is shown, together with the hydrogen bond network these waters make with the protein. Superimposed in black are the equivalent residues of the mannose complex (subunit B in the asymmetric unit). The water molecules clearly mimic the oxygen atoms of bound mannose (black, thick lines). (B) Stereo view of the interactions of mannose in the monosaccharide binding site. The beta-anomeric oxygen position of mannose is drawn in light green, as is the corresponding orientation of the side chain of Glu221. The second conformation of the side chain of Glu221, which also adopts two conformations but not correlated with the anomeric form of the bound mannose is shown in dark green.

Figure 8.
Fig. 8. Comparison between PAL and con A. (A) Comparison between con A and PAL. Stereo view of the binding of M592 (green) to the –1 and M subsites of con A (colored according to atom type). The corresponding situation in PAL is superimposed as shown in thin black lines. (B) Downstream binding sites. Stereo view of the binding of M592 (green) to the +1, +2 and +3 subsites of con A (colored according to atom type). The corresponding situation in PAL is superimposed as shown in thin black lines.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2006, 273, 2407-2420) copyright 2006.

Figures were selected by an automated process.