5L6L

Structure of Caulobacter crescentus VapBC1 bound to operator DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Toxin inhibition in C. crescentus VapBC1 is mediated by a flexible pseudo-palindromic protein motif and modulated by DNA binding.

Bendtsen, K.L.Xu, K.Luckmann, M.Winther, K.S.Shah, S.A.Pedersen, C.N.S.Brodersen, D.E.

(2017) Nucleic Acids Res. 45: 2875-2886

  • DOI: 10.1093/nar/gkw1266
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by ...

    Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric VapBC1 complex from Caulobacter crescentus CB15 both in isolation and bound to its cognate DNA operator sequence at 1.6 and 2.7 Å resolution, respectively. DNA binding is associated with a dramatic architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally, a structure of C-terminally truncated VapB1 bound to VapC1 reveals discrete states of the TA interaction that suggest a structural basis for toxin activation in vivo.


    Organizational Affiliation

    Centre for Bacterial Stress Response and Persistence.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VapB family protein
A, D, E, H
85Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Find proteins for Q9AC34 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9AC34
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ribonuclease VapC
B, C, F, G
128Caulobacter vibrioides (strain ATCC 19089 / CB15)Mutation(s): 0 
Gene Names: vapC
EC: 3.1.-.-
Find proteins for Q9AC35 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Go to UniProtKB:  Q9AC35
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (27-MER)M27Caulobacter vibrioides CB15
Entity ID: 4
MoleculeChainsLengthOrganism
DNA (27-MER)N27Caulobacter vibrioides CB15
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E, F, G, H
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 110.180α = 90.00
b = 144.160β = 90.00
c = 160.540γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
The Lundbeck FoundationDenmarkR173-2014-1182
The Danish National Research FoundationDenmarkDNRF120

Revision History 

  • Version 1.0: 2016-12-28
    Type: Initial release
  • Version 1.1: 2017-01-11
    Type: Database references
  • Version 1.2: 2017-05-03
    Type: Database references
  • Version 1.3: 2018-01-17
    Type: Data collection