New Cyt-like delta-endotoxins from Dickeya dadantii - CytC protein

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report

This is version 1.3 of the entry. See complete history


New Cyt-like delta-endotoxins from Dickeya dadantii: structure and aphicidal activity.

Loth, K.Costechareyre, D.Effantin, G.Rahbe, Y.Condemine, G.Landon, C.da Silva, P.

(2015) Sci Rep 5: 8791-8791

  • DOI: https://doi.org/10.1038/srep08791
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    In the track of new biopesticides, four genes namely cytA, cytB, cytC and cytD encoding proteins homologous to Bacillus thuringiensis (Bt) Cyt toxins have been identified in the plant pathogenic bacteria Dickeya dadantii genome. Here we show that three Cyt-like δ-endotoxins from D. dadantii (CytA, CytB and CytC) are toxic to the pathogen of the pea aphid Acyrthosiphon pisum in terms of both mortality and growth rate. The phylogenetic analysis of the comprehensive set of Cyt toxins available in genomic databases shows that the whole family is of limited taxonomic occurrence, though in quite diverse microbial taxa. From a structure-function perspective the 3D structure of CytC and its backbone dynamics in solution have been determined by NMR. CytC adopts a cytolysin fold, structurally classified as a Cyt2-like protein. Moreover, the identification of a putative lipid binding pocket in CytC structure, which has been probably maintained in most members of the Cyt-toxin family, could support the importance of this lipid binding cavity for the mechanism of action of the whole family. This integrative approach provided significant insights into the evolutionary and functional history of D. dadantii Cyt toxins, which appears to be interesting leads for biopesticides.

  • Organizational Affiliation

    Centre de Biophysique Moléculaire, CNRS UPR 4301, Université d'Orléans, Orléans, F-45071, France.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Type-1Ba cytolytic delta-endotoxin203Dickeya dadantiiMutation(s): 0 
Gene Names: Dda3937_01343
Find proteins for E0SJ33 (Dickeya dadantii (strain 3937))
Explore E0SJ33 
Go to UniProtKB:  E0SJ33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0SJ33
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 500 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-03-18
    Changes: Database references
  • Version 1.2: 2023-06-14
    Changes: Data collection, Database references, Other
  • Version 1.3: 2024-05-15
    Changes: Data collection, Database references