1GNZ

LECTIN I-B4 FROM GRIFFONIA SIMPLICIFOLIA (GS I-B4)METAL FREE FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Isolectins I-A and I-B of Griffonia (Bandeiraea) Simplicifolia. Crystal Structure of Metal-Free Gs I-B(4) and Molecular Basis for Metal Binding and Monosaccharide Specificity.

Lescar, J.Loris, R.Mitchell, E.Gautier, C.Chazalet, V.Cox, V.Wyns, L.Perez, S.Breton, C.Imberty, A.

(2002) J.Biol.Chem. 277: 6608

  • DOI: 10.1074/jbc.M109867200

  • PubMed Abstract: 
  • Seeds from the African legume shrub Griffonia simplicifolia contain several lectins. Among them the tetrameric lectin GS I-B(4) has strict specificity for terminal alpha Gal residues, whereas the closely related lectin GS I-A(4) can also bind to alph ...

    Seeds from the African legume shrub Griffonia simplicifolia contain several lectins. Among them the tetrameric lectin GS I-B(4) has strict specificity for terminal alpha Gal residues, whereas the closely related lectin GS I-A(4) can also bind to alpha GalNAc. These two lectins are commonly used as markers in histology or for research in xenotransplantation. To elucidate the basis for the fine difference in specificity, the amino acid sequences of both lectins have been determined and show 89% identity. The crystal structure of GS I-B(4), determined at 2.5-A resolution, reveals a new quaternary structure that has never been observed in other legume lectins. An unexpected loss of both Ca(2+) and Mn(2+) ions, which are necessary for carbohydrate binding in legume lectins, may be related to a particular amino acid sequence Pro-Glu-Pro in the metal binding loop. Comparison with demetallized concanavalin A reveals a different process for the loss of metal ions and for the subsequent loss of carbohydrate binding activity. The GS I-A x alpha GalNAc and GS I-B x alpha Gal complexes were constructed using homology modeling and docking approaches. The unusual presence of an aromatic amino acid at position 47 (Tyr in I-A and Trp in I-B) explains the strong preference for alpha-anomeric sugars in both isolectins. Alteration at one amino acid position, Ala(106) in I-A versus Glu(106) in I-B, is the basis for the observed specificities toward alpha GalNAc and alpha Gal.


    Organizational Affiliation

    Centre de Recherches sur les Macromolécules Végétales, CNRS, Université Joseph Fourier, BP 53, F-38041 Grenoble cedex 09, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GSI-B4 ISOLECTIN
A
257Griffonia simplicifoliaN/A
Find proteins for Q8W1R6 (Griffonia simplicifolia)
Go to UniProtKB:  Q8W1R6
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.228 
  • Space Group: P 64 2 2
Unit Cell:
Length (Å)Angle (°)
a = 75.927α = 90.00
b = 75.927β = 90.00
c = 190.566γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
SCALEPACKdata scaling
HKLdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-11-29
    Type: Initial release
  • Version 1.1: 2011-09-07
    Type: Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Other, Refinement description, Structure summary, Version format compliance