3VV1

Crystal Structure of Caenorhabditis elegans galectin LEC-6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of preferential binding of fucose-containing saccharide by the Caenorhabditis elegans galectin LEC-6

Makyio, H.Takeuchi, T.Tamura, M.Nishiyama, K.Takahashi, H.Natsugari, H.Arata, Y.Kasai, K.Yamada, Y.Wakatsuki, S.Kato, R.

(2013) Glycobiology 23: 797-805

  • DOI: 10.1093/glycob/cwt017

  • PubMed Abstract: 
  • Galectins are a group of lectins that can bind carbohydrate chains containing β-galactoside units. LEC-6, a member of galectins of Caenorhabditis elegans, binds fucose-containing saccharides. We solved the crystal structure of LEC-6 in complex with g ...

    Galectins are a group of lectins that can bind carbohydrate chains containing β-galactoside units. LEC-6, a member of galectins of Caenorhabditis elegans, binds fucose-containing saccharides. We solved the crystal structure of LEC-6 in complex with galactose-β1,4-fucose (Galβ1-4Fuc) at 1.5 Å resolution. The overall structure of the protein and the identities of the amino-acid residues binding to the disaccharide are similar to those of other galectins. However, further structural analysis and multiple sequence alignment between LEC-6 and other galectins indicate that a glutamic acid residue (Glu67) is important for the preferential binding between LEC-6 and the fucose moiety of the Galβ1-4Fuc unit. Frontal affinity chromatography analysis indicated that the affinities of E67D and E67A mutants for Galβ1-4Fuc are lower than that of wild-type LEC-6. Furthermore, the affinities of Glu67 mutants for an endogenous oligosaccharide, which contains a Galβ1-4Fuc unit, are drastically reduced relative to that of the wild-type protein. We conclude that the Glu67 in the oligosaccharide-binding site assists the recognition of the fucose moiety by LEC-6.


    Organizational Affiliation

    Structural Biology Research Center, Photon Factory, Institute of Materials Structure Science, High Energy Accelerator Research Organization KEK, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein LEC-6
A, B
160Caenorhabditis elegansGene Names: lec-6
Find proteins for Q9N384 (Caenorhabditis elegans)
Go to UniProtKB:  Q9N384
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
A, B
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.179 
  • R-Value Work: 0.147 
  • Space Group: P 63
Unit Cell:
Length (Å)Angle (°)
a = 69.323α = 90.00
b = 69.323β = 90.00
c = 120.131γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHENIXphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-05-22
    Type: Initial release
  • Version 1.1: 2013-07-24
    Type: Database references