1BJQ

THE DOLICHOS BIFLORUS SEED LECTIN IN COMPLEX WITH ADENINE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectin oligomers from Dolichos biflorus.

Hamelryck, T.W.Loris, R.Bouckaert, J.Dao-Thi, M.H.Strecker, G.Imberty, A.Fernandez, E.Wyns, L.Etzler, M.E.

(1999) J Mol Biol 286: 1161-1177

  • DOI: 10.1006/jmbi.1998.2534
  • Primary Citation of Related Structures:  
    1BJQ, 1LU1, 1LU2, 1LUL

  • PubMed Abstract: 
  • The seed lectin (DBL) from the leguminous plant Dolichos biflorus has a unique specificity among the members of the legume lectin family because of its high preference for GalNAc over Gal. In addition, precipitation of blood group A+H substance by DBL is slightly better inhibited by a blood group A trisaccharide (GalNAc(alpha1-3)[Fuc(alpha1-2)]Gal) containing pentasaccharide, and about 40 times better by the Forssman disaccharide (GalNAc(alpha1-3)GalNAc) than by GalNAc ...

    The seed lectin (DBL) from the leguminous plant Dolichos biflorus has a unique specificity among the members of the legume lectin family because of its high preference for GalNAc over Gal. In addition, precipitation of blood group A+H substance by DBL is slightly better inhibited by a blood group A trisaccharide (GalNAc(alpha1-3)[Fuc(alpha1-2)]Gal) containing pentasaccharide, and about 40 times better by the Forssman disaccharide (GalNAc(alpha1-3)GalNAc) than by GalNAc. We report the crystal structures of the DBL-blood group A trisaccharide complex and the DBL-Forssman disaccharide complex.A comparison with the binding sites of Gal-binding legume lectins indicates that the low affinity of DBL for Gal is due to the substitution of a conserved aromatic residue by an aliphatic residue (Leu127). Binding studies with a Leu127Phe mutant corroborate these conclusions. DBL has a higher affinity for GalNAc because the N-acetyl group compensates for the loss of aromatic stacking in DBL by making a hydrogen bond with the backbone amide group of Gly103 and a hydrophobic contact with the side-chains of Trp132 and Tyr104. Some legume lectins possess a hydrophobic binding site that binds adenine and adenine-derived plant hormones, i.e. cytokinins. The exact function of this binding site is unknown, but adenine/cytokinin-binding legume lectins might be involved in storage of plant hormones or plant growth regulation. The structures of DBL in complex with adenine and of the dimeric stem and leaf lectin (DB58) from the same plant provide the first structural data on these binding sites. Both oligomers possess an unusual architecture, featuring an alpha-helix sandwiched between two monomers. In both oligomers, this alpha-helix is directly involved in the formation of the hydrophobic binding site. DB58 adopts a novel quaternary structure, related to the quaternary structure of the DBL heterotetramer, and brings the number of know legume lectin dimer types to four.


    Related Citations: 
    • Crystallization of Two Related Lectins from the Legume Plant Dolichos Biflorus
      Dao-Thi, M.-H., Hamelryck, T.W., Bouckaert, J., Korber, F., Burkow, V., Poortmans, F., Etzler, M., Strecker, G., Wyns, L., Loris, R.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 1446

    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vlaams Interuniversitair Instituur voor Biotechnologie, Vrije Universiteit Brussel, Paardenstraat 65, Sint-Genesius-Rode, B-1640, Belgium. thamelry@vub.ac.be



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LECTIN
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H
253Vigna unguiculata subsp. cylindricaMutation(s): 0 
UniProt
Find proteins for P05045 (Vigna unguiculata subsp. cylindrica)
Explore P05045 
Go to UniProtKB:  P05045
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05045
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADE
Query on ADE

Download Ideal Coordinates CCD File 
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
CA [auth G],
FA [auth H],
K [auth A],
N [auth B],
Q [auth C],
T [auth D],
W [auth E],
Z [auth F]
ADENINE
C5 H5 N5
GFFGJBXGBJISGV-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
BA [auth G],
EA [auth H],
J [auth A],
M [auth B],
P [auth C],
S [auth D],
V [auth E],
Y [auth F]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
AA [auth G],
DA [auth H],
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.219 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.377α = 90
b = 116.135β = 90
c = 224.62γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1998-12-30
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance