PDBsum entry 2vuv

Sugar binding protein

PDB id: 2vuv

Contents

Protein chain

129 a.a. *

Ligands

GOL ×2

CIT

Metals

_CA

Waters ×174

* Residue conservation analysis

PDB id:

2vuv

Name:

Sugar binding protein

Title:

Crystal structure of codakine at 1.3a resolution

Structure:

Codakine. Chain: a. Fragment: residues 20-148

Source:

Codakia orbicularis. Organism_taxid: 13016

Resolution:

1.30Å R-factor: 0.145 R-free: 0.161

Authors:

J.P.Gourdine,G.C.Cioci,L.Miguet,C.Unverzagt,A.Varrot,C.Gauthier, E.J.Smith-Ravin,A.Imberty

Key ref:

J.P.Gourdine et al. (2008). High Affinity Interaction between a Bivalve C-type Lectin and a Biantennary Complex-type N-Glycan Revealed by Crystallography and Microcalorimetry. J Biol Chem, 283, 30112-30120. PubMed id: 18687680 DOI: 10.1074/jbc.M804353200

Date:

30-May-08 Release date: 05-Aug-08

Protein chain

Q3KVL7  (Q3KVL7_9BIVA) -  Codakine from Codakia orbicularis

Seq: 148 a.a.

Struc: 129 a.a.*

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

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1074/jbc.M804353200

J Biol Chem 283:30112-30120 (2008)

PubMed id: 18687680

High Affinity Interaction between a Bivalve C-type Lectin and a Biantennary Complex-type N-Glycan Revealed by Crystallography and Microcalorimetry.

J.P.Gourdine, G.Cioci, L.Miguet, C.Unverzagt, D.V.Silva, A.Varrot, C.Gautier, E.J.Smith-Ravin, A.Imberty.

ABSTRACT

Codakine is an abundant 14-kDa mannose-binding C-type lectin isolated from the gills of the sea bivalve Codakia orbicularis. Binding studies using inhibition of hemagglutination indicated specificity for mannose and fucose monosaccharides. Further experiments using a glycan array demonstrated, however, a very fine specificity for N-linked biantennary complex-type glycans. An unusually high affinity was measured by titration microcalorimetry performed with a biantennary Asn-linked nonasaccharide. The crystal structure of the native lectin at 1.3A resolution revealed a new type of disulfide-bridged homodimer. Each monomer displays three intramolecular disulfide bridges and contains only one calcium ion located in the canonical binding site that is occupied by a glycerol molecule. The structure of the complex between Asn-linked nonasaccharide and codakine has been solved at 1.7A resolution. All residues could be located in the electron density map, except for the capping beta1-4-linked galactosides. The alpha1-6-linked mannose binds to calcium by coordinating the O3 and O4 hydroxyl groups. The GlcNAc moiety of the alpha1,6 arm engages in several hydrogen bonds with the protein, whereas the GlcNAc on the other antenna is stacked against Trp(108), forming an extended binding site. This is the first structural report for a bivalve lectin.

Selected figure(s)

Figure 4.
Crystal structure of codakine complexed with nona-Asn. A, representation of the final maximum likelihood weighted 2 mF[o] - DF[o] electron density map (contoured at 1.0σ, 0.34 e Å^-3 for the nona-Asn oligosaccharide. B, hydrogen bond network between oligosaccharide and codakine amino acids. Intramolecular hydrogen bonds of the nonasaccharide are represented by blue dashed lines. C, comparison of oligosaccharide binding site in codakine (left) and DC-SIGN (right) (43). The star indicates the position of the calcium ion. Electrostatic surface was calculated with APBS (56).

Figure 5.
Comparison of dimerization modes for invertebrate lectins. Calcium ions are represented as dark spheres, and intermolecular disulfide bridges, when present, are colored in black. A, codakine complexed with nona-Asn. B, tunicate (P. misakiensis) lectin TL14 complexed with galactose (50). C, sea cucumber (C. echinata) CEL-I lectin complexed with N-acetyl-galactosamine (53).

The above figures are reprinted from an Open Access publication published by the ASBMB: J Biol Chem (2008, 283, 30112-30120) copyright 2008.

Figures were selected by the author.