1G7Y

THE CRYSTAL STRUCTURE OF THE 58KD VEGETATIVE LECTIN FROM THE TROPICAL LEGUME DOLICHOS BIFLORUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Weak protein-protein interactions in lectins: the crystal structure of a vegetative lectin from the legume Dolichos biflorus.

Buts, L.Dao-Thi, M.H.Loris, R.Wyns, L.Etzler, M.Hamelryck, T.

(2001) J.Mol.Biol. 309: 193-201

  • DOI: 10.1006/jmbi.2001.4639
  • Primary Citation of Related Structures:  1G8W, 1G9F

  • PubMed Abstract: 
  • The legume lectins are widely used as a model system for studying protein-carbohydrate and protein-protein interactions. They exhibit a fascinating quaternary structure variation, which becomes important when they interact with multivalent glycoconju ...

    The legume lectins are widely used as a model system for studying protein-carbohydrate and protein-protein interactions. They exhibit a fascinating quaternary structure variation, which becomes important when they interact with multivalent glycoconjugates, for instance those on cell surfaces. Recently, it has become clear that certain lectins form weakly associated oligomers. This phenomenon may play a role in the regulation of receptor crosslinking and subsequent signal transduction. The crystal structure of DB58, a dimeric lectin from the legume Dolichos biflorus reveals a separate dimer of a previously unobserved type, in addition to a tetramer consisting of two such dimers. This tetramer resembles that formed by DBL, the seed lectin from the same plant. A single amino acid substitution in DB58 affects the conformation and flexibility of a loop in the canonical dimer interface. This disrupts the formation of a stable DBL-like tetramer in solution, but does not prohibit its formation in suitable conditions, which greatly increases the possibilities for the cross-linking of multivalent ligands. The non-canonical DB58 dimer has a buried symmetrical alpha helix, which can be present in the crystal in either of two antiparallel orientations. Two existing structures and datasets for lectins with similar quaternary structures were reconsidered. A central alpha helix could be observed in the soybean lectin, but not in the leucoagglutinating lectin from Phaseolus vulgaris. The relative position and orientation of the carbohydrate-binding sites in the DB58 dimer may affect its ability to crosslink mulitivalent ligands, compared to the other legume lectin dimers.


    Related Citations: 
    • Carbohydrate binding, quaternary structure and a novel hydrophobic binding site in two legume lectins 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
    • Crystallisation of two related lectins from the legume plant Dolichos biflorus
      Dao-Thi, M.,Hamelryck, T.W.,Bouckaert, J.,Koerber, F.,Burkow, V.,Poortmans, F.,Etzler, M.,Strecker, G.,Wyns, L.,Loris, R.
      (1998) Acta Crystallogr.,Sect.D 54: 1446


    Organizational Affiliation

    ULTR-Ultrastructure Department, Vrije Universiteit Brussel, Sint-Genesius-Rode Belgium. lieven@ultr.vub.ac.be




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
STEM/LEAF LECTIN DB58
A, B, C, D, E, F
253Vigna unguiculata subsp. cylindricaN/A
Find proteins for P19588 (Vigna unguiculata subsp. cylindrica)
Go to UniProtKB:  P19588
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

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Download CCD File 
A, B, C, D, E, F
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, B, C, D, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

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Download CCD File 
B, E
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
NAG
Query on NAG

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Download CCD File 
B, C, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

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Download CCD File 
C
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.941α = 90.00
b = 130.272β = 90.00
c = 137.124γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-11-29
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance