PDBsum entry 1ulm

Sugar binding protein

PDB id: 1ulm

Contents

Protein chains

82 a.a. *

Ligands

NAG-NAG-NAG ×2

Waters ×122

* Residue conservation analysis

PDB id:

1ulm

Name:

Sugar binding protein

Title:

Crystal structure of pokeweed lectin-d2 complexed with tri-n- acetylchitotriose

Structure:

Lectin-d2. Chain: a, b

Source:

Phytolacca americana. American pokeweed. Organism_taxid: 3527. Tissue: roots

Resolution:

1.80Å R-factor: 0.195 R-free: 0.234

Authors:

M.Hayashida,T.Fujii,M.Ishiguro,Y.Hata

Key ref:

M.Hayashida et al. (2003). Similarity between protein-protein and protein-carbohydrate interactions, revealed by two crystal structures of lectins from the roots of pokeweed. J Mol Biol, 334, 551-565. PubMed id: 14623194 DOI: 10.1016/j.jmb.2003.09.076

Date:

12-Sep-03 Release date: 23-Dec-03

Protein chains

P83790  (LED2_PHYAM) -  Lectin-D2 from Phytolacca americana

Seq: 82 a.a.

Struc: 82 a.a.

DOI no: 10.1016/j.jmb.2003.09.076

J Mol Biol 334:551-565 (2003)

PubMed id: 14623194

Similarity between protein-protein and protein-carbohydrate interactions, revealed by two crystal structures of lectins from the roots of pokeweed.

M.Hayashida, T.Fujii, M.Hamasu, M.Ishiguro, Y.Hata.

ABSTRACT

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.

Selected figure(s)

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.

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.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 334, 551-565) copyright 2003.

Figures were selected by an automated process.