1SR4

Crystal Structure of the Haemophilus ducreyi cytolethal distending toxin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Assembly and Function of a Bacterial Genotoxin

Nesic, D., Hsu, Y., Stebbins, C.E.

(2004) Nature 429: 429-433

  • DOI: 10.1038/nature02532

  • PubMed Abstract: 

    • The tripartite cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells. The subunits CdtA and CdtC associate with the nuclease CdtB to form a holotoxin that translocates CdtB into the host cell, where it acts as ...

    The tripartite cytolethal distending toxin (CDT) induces cell cycle arrest and apoptosis in eukaryotic cells. The subunits CdtA and CdtC associate with the nuclease CdtB to form a holotoxin that translocates CdtB into the host cell, where it acts as a genotoxin by creating DNA lesions. Here we show that the crystal structure of the holotoxin from Haemophilus ducreyi reveals that CDT consists of an enzyme of the DNase-I family, bound to two ricin-like lectin domains. CdtA, CdtB and CdtC form a ternary complex with three interdependent molecular interfaces, characterized by globular, as well as extensive non-globular, interactions. The lectin subunits form a deeply grooved, highly aromatic surface that we show to be critical for toxicity. The holotoxin possesses a steric block of the CdtB active site by means of a non-globular extension of the CdtC subunit, and we identify putative DNA binding residues in CdtB that are essential for toxin activity.

    Organizational Affiliation: 

    Laboratory of Structural Microbiology, The Rockefeller University, New York 10021, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cytolethal distending toxin subunit A
A
206Haemophilus ducreyi (strain 35000HP / ATCC 700724)Mutation(s): 0 
Gene Names: cdtA
Find proteins for O06522 (Haemophilus ducreyi (strain 35000HP / ATCC 700724))
Go to UniProtKB:  O06522
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
cytolethal distending toxin protein B
B
261Haemophilus ducreyiMutation(s): 0 
Gene Names: cdtB
Find proteins for O06523 (Haemophilus ducreyi)
Go to UniProtKB:  O06523
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
cytolethal distending toxin protein C
C
166Haemophilus ducreyiMutation(s): 0 
Gene Names: cdtC
Find proteins for O06524 (Haemophilus ducreyi)
Go to UniProtKB:  O06524
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BR
Query on BR
Download SDF File 
Download CCD File 
A, B, C
BROMIDE ION
Br
CPELXLSAUQHCOX-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 71.652α = 90.00
b = 75.653β = 90.00
c = 121.637γ = 90.00
Software Package:
Software NamePurpose
SOLVEphasing
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-06-15
    Type: Initial release
  • Version 1.1: 2008-04-29
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance