5L6L

Structure of Caulobacter crescentus VapBC1 bound to operator DNA

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 

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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: https://doi.org/10.1093/nar/gkw1266
  • Primary Citation of Related Structures:  
    5K8J, 5L6L, 5L6M

  • 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 stimulating DNA binding through direct interaction with the antitoxin ...

    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: 

    Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 10c, DK-8000 Aarhus C, Denmark.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
VapB family proteinA, D, E, H85Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: CC_0032
UniProt
Find proteins for Q9AC34 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9AC34 
Go to UniProtKB:  Q9AC34
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AC34
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ribonuclease VapCB, C, F, G128Caulobacter vibrioides CB15Mutation(s): 0 
Gene Names: vapC, CC_0031
EC: 3.1
UniProt
Find proteins for Q9AC35 (Caulobacter vibrioides (strain ATCC 19089 / CB15))
Explore Q9AC35 
Go to UniProtKB:  Q9AC35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9AC35
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNA (27-MER)I [auth M]27Caulobacter vibrioides CB15
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsLengthOrganismImage
DNA (27-MER)J [auth N]27Caulobacter vibrioides CB15
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, D, E, H L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.181 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.18α = 90
b = 144.16β = 90
c = 160.54γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

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

Revision History  (Full details and data files)

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