PDBsum entry 1vbp

Plant protein

PDB id: 1vbp

Contents

Protein chains

149 a.a. *

Ligands

MAN-MAN-MAN-MAN

MAN-MAN-MAN

SO4 ×5

Waters ×1

* Residue conservation analysis

PDB id:

1vbp

Name:

Plant protein

Title:

Crystal structure of artocarpin-mannopentose complex

Structure:

Artocarpin. Chain: a, b

Source:

Artocarpus integer. Organism_taxid: 3490. Tissue: seeds

Biol. unit:

Hexamer (from PDB file)

Resolution:

3.50Å R-factor: 0.263 R-free: 0.292

Authors:

A.A.Jeyaprakash,A.Srivastav,A.Surolia,M.Vijayan

Key ref:

A.A.Jeyaprakash et al. (2004). Structural basis for the carbohydrate specificities of artocarpin: variation in the length of a loop as a strategy for generating ligand specificity. J Mol Biol, 338, 757-770. PubMed id: 15099743 DOI: 10.1016/j.jmb.2004.03.040

Date:

28-Feb-04 Release date: 15-Jun-04

Protein chains

Q7M1T4  (Q7M1T4_ARTIN) -  Mannose-specific lectin KM+ from Artocarpus integer

Seq: 149 a.a.

Struc: 149 a.a.*

* PDB and UniProt seqs differ at 7 residue positions (black crosses)

DOI no: 10.1016/j.jmb.2004.03.040

J Mol Biol 338:757-770 (2004)

PubMed id: 15099743

Structural basis for the carbohydrate specificities of artocarpin: variation in the length of a loop as a strategy for generating ligand specificity.

A.A.Jeyaprakash, A.Srivastav, A.Surolia, M.Vijayan.

ABSTRACT

Artocarpin, a tetrameric lectin of molecular mass 65 kDa, is one of the two lectins extracted from the seeds of jackfruit. The structures of the complexes of artocarpin with mannotriose and mannopentose reported here, together with the structures of artocarpin and its complex with Me-alpha-mannose reported earlier, show that the lectin possesses a deep-seated binding site formed by three loops. The binding site can be considered as composed of two subsites; the primary site and the secondary site. Interactions at the primary site composed of two of the loops involve mainly hydrogen bonds, while those at the secondary site comprising the third loop are primarily van der Waals in nature. Mannotriose in its complex with the lectin interacts through all the three mannopyranosyl residues; mannopentose interacts with the protein using at least three of the five mannose residues. The complexes provide a structural explanation for the carbohydrate specificities of artocarpin. A detailed comparison with the sugar complexes of heltuba, the only other mannose-specific jacalin-like lectin with known three-dimensional structure in sugar-bound form, establishes the role of the sugar-binding loop constituting the secondary site, in conferring different specificities at the oligosaccharide level. This loop is four residues longer in artocarpin than in heltuba, providing an instance where variation in loop length is used as a strategy for generating carbohydrate specificity.

Selected figure(s)

Figure 3.
Figure 3. Stereo view of the superposition of the sugar-binding region of mannotriose complex (violet) on that in the Me-a-Man complex (green). Interactions between the mannotriose and the lectin are shown.

Figure 5.
Figure 5. Surface representation of the sugar-binding site with modelled (a) Mana1-2Man (conformers I; blue, II; pink), (b) Mana1-6Man (conformers I; blue, II; gold, III; brown), (c) Gn[2]Mn[3] and (d) horseradish peroxidase oligosaccharide.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 338, 757-770) copyright 2004.

Figures were selected by an automated process.