4ELZ

CCDBVFI:GYRA14VFI


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Alternative interactions define gyrase specificity in the CcdB family.

De Jonge, N.Simic, M.Buts, L.Haesaerts, S.Roelants, K.Garcia-Pino, A.Sterckx, Y.De Greve, H.Lah, J.Loris, R.

(2012) Mol.Microbiol. 84: 965-978

  • DOI: 10.1111/j.1365-2958.2012.08069.x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toxin-antitoxin (TA) modules are small operons associated with stress response of bacteria. F-plasmid CcdB(F) was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved ...

    Toxin-antitoxin (TA) modules are small operons associated with stress response of bacteria. F-plasmid CcdB(F) was the first TA toxin for which its target, gyrase, was identified. Plasmidic and chromosomal CcdBs belong to distinct families. Conserved residues crucial for gyrase poisoning activity of plasmidic CcdBs are not conserved among these families. Here we show that the chromosomal CcdB(Vfi) from Vibrio fischeri is an active gyrase poison that interacts with its target via an alternative energetic mechanism. Changes in the GyrA14-binding surface of the Vibrio and F-plasmid CcdB family members illustrate neutral drift where alternative interactions can be used to achieve the same functionality. Differences in affinity between V. fischeri and F-plasmid CcdB for gyrase and their corresponding CcdA antitoxin possibly reflect distinct roles for TA modules located on plasmids and chromosomes.


    Organizational Affiliation

    Structural Biology Brussels, Department of Biotechnology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit A
A, B
153Aliivibrio fischeri (strain ATCC 700601 / ES114)Mutation(s): 0 
Gene Names: gyrA
EC: 5.99.1.3
Find proteins for Q5E5J7 (Aliivibrio fischeri (strain ATCC 700601 / ES114))
Go to UniProtKB:  Q5E5J7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
CcdB
C, D
105Aliivibrio fischeri (strain MJ11)Mutation(s): 0 
Find proteins for B5EU32 (Aliivibrio fischeri (strain MJ11))
Go to UniProtKB:  B5EU32
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.195 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.505α = 90.00
b = 94.590β = 90.00
c = 120.502γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
DENZOdata reduction
SCALEPACKdata scaling
MAR345dtbdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release