PDBsum entry: 1k7v

Sugar binding protein

PDB-id: 1k7v

Biological unit* = asymmetric unit,
as shown
(*as deduced by PQS)

Contents

Description

Header details

Header records

References

PROCHECK

Protein chains

171 a.a. *

Ligands

NAG-GAL-BGC ×2

Waters ×120

* Residue conservation analysis

Tools

Clefts Calculation

PDB id:

1k7v

Name:

Sugar binding protein

Title:

Crystal structure analysis of crosslinked-wga3/glcnacbeta1, 6galbeta1,4glc

Structure:

Agglutinin isolectin 3. Chain: a, b. Synonym: wga3

Source:

Triticum aestivum. Bread wheat. Organism_taxid: 4565

Biological unit:

Dimer (from PQS)

UniProt:

Chains A, B: P10969 (AGI3_WHEAT)

Seq:

186 a.a.

Struc:

171 a.a.*

Key:	PfamA domain
Secondary structure	CATH domain

* PDB and UniProt seqs differ at 1 residue position (black cross)

Resolution:

2.20Å

R-factor:

0.232

R-free:

0.310

Authors:

M.Muraki,M.Ishimura,K.Harata

Key ref:

M.Muraki et al. (2002). Interactions of wheat-germ agglutinin with GlcNAc beta 1,6Gal sequence.. Biochim Biophys Acta, 1569, 10-20. [PubMed id: 11853952] [DOI: 10.1016/S0304-4165(01)00231-8]

Date:

22-Oct-01

Release date:

03-Apr-02

Related entries:

1wgt
1wgt contains wheat-germ-agglutinin 3 (wga3)
1k7t
1k7t contains crosslinked-wga3/glcnacbeta1,6gal complex
1k7u
1k7u contains crosslinked-wga3/glcnacbeta1,4glcnac complex

Quick_links

Procheck

Clefts

Surface

Key reference

DOI no: 10.1016/S0304-4165(01)00231-8

Biochim Biophys Acta 1569:10-20 (2002)

PubMed id: 11853952

Interactions of wheat-germ agglutinin with GlcNAc beta 1,6Gal sequence.

M.Muraki, M.Ishimura, K.Harata.

ABSTRACT

The interactions of wheat-germ agglutinin (WGA) with the GlcNAc beta 1,6Gal sequence, a characteristic component of branched poly-N-acetyllactosaminoglycans, were investigated using isothermal titration calorimetry and X-ray crystallography. GlcNAc beta 1,6Gal exhibited an affinity greater than GlcNAc beta 1,4GlcNAc to all WGA isolectins, whereas Gal beta 1,6GlcNAc showed much less affinity than GlcNAc beta 1,4GlcNAc. X-ray structural analyses of the glutaraldehyde-crosslinked WGA isolectin 3 crystals in complex with GlcNAc beta 1,6Gal, GlcNAc beta 1,4GlcNAc and GlcNAc beta 1,6Gal beta 1,4Glc were performed at 2.4, 2.2 and 2.2 A resolution, respectively. In spite of different glycosidic linkages, GlcNAc beta 1,6Gal and GlcNAc beta 1,4GlcNAc exhibited basically similar binding modes to each other, in contact with side chains of two aromatic residues, Tyr64 and His66. However, the conformations of the ligands in the two primary binding sites were not always identical. GlcNAc beta 1,6Gal showed more extensive variation in the parameters defining the glycosidic linkage structure compared to GlcNAc beta 1,4GlcNAc, demonstrating large conformational flexibility of the former ligand in the interaction with WGA. The difference in the ligand binding conformation was accompanied by alterations of the side chain conformation of the amino acid residues involved in the interactions. The hydrogen bond between Ser62 and the non-reducing end GlcNAc was always observed regardless of the ligand type, indicating the key role of this interaction. In addition to the hydrogen bonding and van der Waals interactions, CH--pi interactions involving Tyr64, His66 and Tyr73 are suggested to play an essential role in determining the ligand binding conformation in all complexes. One of the GlcNAc beta 1,6Gal ligands had no crystal packing contact with another WGA molecule, therefore the conformation might be more relevant to the interaction mode in solution.