Pectate lyase B from Verticillium dahliae

Experimental Data Snapshot

  • Resolution: 1.20 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


The specificity of pectate lyase VdPelB from Verticilium dahliae is highlighted by structural, dynamical and biochemical characterizations.

Safran, J.Ung, V.Bouckaert, J.Habrylo, O.Molinie, R.Fontaine, J.X.Lemaire, A.Voxeur, A.Pilard, S.Pau-Roblot, C.Mercadante, D.Pelloux, J.Senechal, F.

(2023) Int J Biol Macromol 231: 123137-123137

  • DOI: https://doi.org/10.1016/j.ijbiomac.2023.123137
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Pectins, complex polysaccharides and major components of the plant primary cell wall, can be degraded by pectate lyases (PLs). PLs cleave glycosidic bonds of homogalacturonans (HG), the main pectic domain, by β-elimination, releasing unsaturated oligogalacturonides (OGs). To understand the catalytic mechanism and structure/function of these enzymes, we characterized VdPelB from Verticillium dahliae. We first solved the crystal structure of VdPelB at 1.2 Å resolution showing that it is a right-handed parallel β-helix structure. Molecular dynamics (MD) simulations further highlighted the dynamics of the enzyme in complex with substrates that vary in their degree of methylesterification, identifying amino acids involved in substrate binding and cleavage of non-methylesterified pectins. We then biochemically characterized wild type and mutated forms of VdPelB. Pectate lyase VdPelB was most active on non-methylesterified pectins, at pH 8.0 in presence of Ca 2+ ions. The VdPelB-G125R mutant was most active at pH 9.0 and showed higher relative activity compared to native enzyme. The OGs released by VdPelB differed to that of previously characterized PLs, showing its peculiar specificity in relation to its structure. OGs released from Verticillium-partially tolerant and sensitive flax cultivars differed which could facilitate the identification VdPelB-mediated elicitors of defence responses.

  • Organizational Affiliation

    UMR INRAE 1158 BioEcoAgro - Biologie des Plantes et Innovation, Université de Picardie Jules Verne, UFR des Sciences, 33 Rue St Leu, 80039 Amiens, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pectate lyase B
A, B
343Verticillium dahliae VdLs.17Mutation(s): 0 
Gene Names: VDAG_04718
Find proteins for G2X3Y1 (Verticillium dahliae (strain VdLs.17 / ATCC MYA-4575 / FGSC 10137))
Explore G2X3Y1 
Go to UniProtKB:  G2X3Y1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG2X3Y1
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MAN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
H [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B]
C6 H12 O6
Query on PEG

Download Ideal Coordinates CCD File 
C4 H10 O3
Query on CA

Download Ideal Coordinates CCD File 
C [auth A],
J [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.20 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.89α = 90
b = 59.69β = 96.35
c = 93.87γ = 90
Software Package:
Software NamePurpose
pointlessdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Regional Development FundEuropean Union--
Agence Nationale de la Recherche (ANR)FranceCARAPEC-Region Hauts de France

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-13
    Type: Initial release
  • Version 1.1: 2023-02-01
    Changes: Database references
  • Version 1.2: 2024-02-07
    Changes: Data collection, Refinement description