1IOA

ARCELIN-5, A LECTIN-LIKE DEFENSE PROTEIN FROM PHASEOLUS VULGARIS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of arcelin-5, a lectin-like defense protein from Phaseolus vulgaris

Hamelryck, T.Poortmans, F.Goossens, A.Angenon, G.Van Montagu, M.Wyns, L.Loris, R.

(1996) J.Biol.Chem. 271: 32796-32802


  • PubMed Abstract: 
  • In the seeds of the legume plants, a class of sugar-binding proteins with high structural and sequential identity is found, generally called the legume lectins. The seeds of the common bean (Phaseolus vulgaris) contain, besides two such lectins, a le ...

    In the seeds of the legume plants, a class of sugar-binding proteins with high structural and sequential identity is found, generally called the legume lectins. The seeds of the common bean (Phaseolus vulgaris) contain, besides two such lectins, a lectin-like defense protein called arcelin, in which one sugar binding loop is absent. Here we report the crystal structure of arcelin-5 (Arc5), one of the electrophoretic variants of arcelin, solved at a resolution of 2.7 A. The R factor of the refined structure is 20.6%, and the free R factor is 27.1%. The main difference between Arc5 and the legume lectins is the absence of the metal binding loop. The bound metals are necessary for the sugar binding capabilities of the legume lectins and stabilize an Ala-Asp cis-peptide bond. Surprisingly, despite the absence of the metal binding site in Arc5, this cis-peptide bond found in all legume lectin structures is still present, although the Asp residue has been replaced by a Tyr residue. Despite the high identity between the different legume lectin sequences, they show a broad range of quaternary structures. The structures of three different dimers and three different tetramers have been solved. Arc5 crystallized as a monomer, bringing the number of known quaternary structures to seven.


    Related Citations: 
    • The Crystallographic Structure of Phytohemagglutinin-L
      Hamelryck, T.W.,Dao-Thi, M.H.,Poortmans, F.,Chrispeels, M.J.,Wyns, L.,Loris, R.
      (1996) J.Biol.Chem. 271: 20479
    • Lectins, Lectin Genes, and Their Role in Plant Defense
      Chrispeels, M.J.,Raikhel, N.V.
      (1991) Plant Cell 3: 1


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ARCELIN-5A
A, B
240Phaseolus vulgarisGene Names: ARC5A (ARC5-1, ARC5-I)
Find proteins for Q42460 (Phaseolus vulgaris)
Go to UniProtKB:  Q42460
Small Molecules
Ligands 2 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
NAG
Query on NAG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.300α = 90.00
b = 94.500β = 94.97
c = 82.900γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
MADNESdata reduction
X-PLORrefinement
X-PLORphasing
MADNESdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1996-12-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2014-11-26
    Type: Other