PDBsum entry: 1uln

Sugar binding protein

PDB id: 1uln

Contents

Protein chain

82 a.a. *

Waters ×133

* Residue conservation analysis

PDB id:

1uln

Name:

Sugar binding protein

Title:

Crystal structure of pokeweed lectin-d1

Structure:

Lectin-d. Chain: a. Synonym: lectin-d1

Source:

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

Resolution:

1.65Å R-factor: 0.172 R-free: 0.205

Authors:

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

Key ref:

T.Fujii et al. (2004). Structures of two lectins from the roots of pokeweed (Phytolacca americana). Acta Crystallogr D Biol Crystallogr, 60, 665-673. PubMed id: 15039554 DOI: 10.1107/S090744490400232X

Date:

16-Sep-03 Release date: 13-Apr-04

Protein chain

P83790  (LED2_PHYAM) -  Lectin-D2

Seq: 82 a.a.

Struc: 82 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: cell wall macromolecule catabolic process (4 terms)
• Biochemical function: sugar binding (3 terms)

DOI no: 10.1107/S090744490400232X

Acta Crystallogr D Biol Crystallogr 60:665-673 (2004)

PubMed id: 15039554

Structures of two lectins from the roots of pokeweed (Phytolacca americana).

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

ABSTRACT

Pokeweed lectin (PL), a lectin specific for N-acetylglucosamine-containing saccharides, stimulates peripheral lymphocytes to undergo mitosis by binding to their cell surfaces. Four types of lectins have been isolated from the roots of pokeweed (Phytolacca americana) and shown to contain homologous domains but to have different molecular sizes and biological properties. PL-D, the smallest lectin in the group, has two isolectins, PL-D1 and PL-D2. PL-D1 consists of 84 amino-acid residues, while PL-D2 is identical to PL-D1 in sequence except for the lack of two C-terminal residues, Leu83 and Thr84. The crystal structures of PL-D1 and PL-D2 were solved by the molecular-replacement method and refined to 1.65 and 1.5 A resolution with R factors of 17.2 and 17.6%, respectively. The PL-Ds are composed of two repetitive chitin-binding domains, each of which has four S-S bridges and one putative carbohydrate-binding site. The two carbohydrate-binding sites in PL-D are located on one side of the molecule. The relative orientation of the two domains in PL-D1 differs from that in PL-D2. Two C-terminal residues of PL-D1 are invisible in the present crystal structure, indicating the flexibility of the region. PL-D2 has a Ca2+ ion bound to the C-terminus on the molecular surface. A wide distribution of acidic residues is characteristically observed on one side of the C-terminal region of PL-D.

Selected figure(s)

Figure 4.
Figure 4 Structural comparison between carbohydrate-binding sites: (a) domain I of PL-D2, (b) domain II of PL-D2, (c) domain I of UDA6 complexed with tri-N-acetylchitotriose and (d) domain II of UDA6 complexed with tri-N-acetylchitotriose. Each site is shown in almost the same orientation. Thick ball-and-stick models show carbohydrate-binding residues. Disulfide bridges are shown as orange sticks. Thin ball-and-stick models show tri-N-acetylchitotriose. The hydrogen bonds between the saccharide molecule and the protein are shown by dotted lines coloured cyan.

Figure 7.
Figure 7 Distribution of acidic residues in PL-D2. (a) C^ -trace model with charged residues. The carbohydrate-binding residues, acidic residues and basic residues are shown as grey, light red and light blue ball-and-stick representations, respectively. Disulfide bridges are shown as orange sticks. (b) Electrostatic potential surface. The molecule is shown in the same orientation as that in (a). The potentials are coloured from -10kT (red) to +10kT (blue).

The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2004, 60, 665-673) copyright 2004.

Figures were selected by an automated process.