1X75

CcdB:GyrA14 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis of Gyrase Poisoning by the Addiction Toxin CcdB

Dao-Thi, M.H.Van Melderen, L.De Genst, E.Afif, H.Buts, L.Wyns, L.Loris, R.

(2005) J.Mol.Biol. 348: 1091-1102

  • DOI: 10.1016/j.jmb.2005.03.049

  • PubMed Abstract: 
  • Gyrase is an ubiquitous bacterial enzyme that is responsible for disentangling DNA during DNA replication and transcription. It is the target of the toxin CcdB, a paradigm for plasmid addiction systems and related bacterial toxin-antitoxin systems. T ...

    Gyrase is an ubiquitous bacterial enzyme that is responsible for disentangling DNA during DNA replication and transcription. It is the target of the toxin CcdB, a paradigm for plasmid addiction systems and related bacterial toxin-antitoxin systems. The crystal structure of CcdB and the dimerization domain of the A subunit of gyrase (GyrA14) dictates an open conformation for the catalytic domain of gyrase when CcdB is bound. The action of CcdB is one of a wedge that stabilizes a dead-end covalent gyrase:DNA adduct. Although CcdB and GyrA14 form a globally symmetric complex where the two 2-fold axes of both dimers align, the complex is asymmetric in its details. At the centre of the interaction site, the Trp99 pair of CcdB stacks with the Arg462 pair of GyrA14, explaining why the Arg462Cys mutation in the A subunit of gyrase confers resistance to CcdB. Overexpression of GyrA14 protects Escherichia coli cells against CcdB, mimicking the action of the antidote CcdA.


    Organizational Affiliation

    Laboratorium voor Ultrastructuur, Vrije Universiteit Brussel and Department of Molecular and Cellular Interactions, Vlaams Instituut voor Biotechnologie, Building E, Pleinlaan 2, B-1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, B
132Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: gyrA (hisW, nalA, parD)
EC: 5.6.2.3
Find proteins for P0AES4 (Escherichia coli (strain K12))
Go to UniProtKB:  P0AES4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Cytotoxic protein ccdB
C, D
101Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: ccdB (G, letB, letD)
Find proteins for P62554 (Escherichia coli (strain K12))
Go to UniProtKB:  P62554
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.224 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.124α = 90.00
b = 83.344β = 90.00
c = 110.919γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
CCP4data scaling
MOSFLMdata reduction
CNSrefinement
TRUNCATEdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-05-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance