3ZVK

Crystal structure of VapBC2 from Rickettsia felis bound to a DNA fragment from their promoter


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal Structure of the DNA-Bound Vapbc2 Antitoxin/Toxin Pair from Rickettsia Felis.

Mate, M.J.Vincentelli, R.Foos, N.Raoult, D.Cambillau, C.Ortiz-Lombardia, M.

(2012) Nucleic Acids Res 40: 3245

  • DOI: 10.1093/nar/gkr1167
  • Primary Citation of Related Structures:  
    3ZVK

  • PubMed Abstract: 
  • Besides their commonly attributed role in the maintenance of low-copy number plasmids, toxin/antitoxin (TA) loci, also called 'addiction modules', have been found in chromosomes and associated to a number of biological functions such as: reduction of ...

    Besides their commonly attributed role in the maintenance of low-copy number plasmids, toxin/antitoxin (TA) loci, also called 'addiction modules', have been found in chromosomes and associated to a number of biological functions such as: reduction of protein synthesis, gene regulation and retardation of cell growth under nutritional stress. The recent discovery of TA loci in obligatory intracellular species of the Rickettsia genus has prompted new research to establish whether they work as stress response elements or as addiction systems that might be toxic for the host cell. VapBC2 is a TA locus from R. felis, a pathogen responsible for flea-borne spotted fever in humans. The VapC2 toxin is a PIN-domain protein, whereas the antitoxin, VapB2, belongs to the family of swapped-hairpin β-barrel DNA-binding proteins. We have used a combination of biophysical and structural methods to characterize this new toxin/antitoxin pair. Our results show how VapB2 can block the VapC2 toxin. They provide a first structural description of the interaction between a swapped-hairpin β-barrel protein and DNA. Finally, these results suggest how the VapC2/VapB2 molar ratio can control the self-regulation of the TA locus transcription.


    Organizational Affiliation

    Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques, Campus de Luminy, Case 932, 13288 Marseille Cedex 09, France.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TOXIN OF TOXIN-ANTITOXIN SYSTEMABCD134Rickettsia felisMutation(s): 1 
EC: 3.1
Find proteins for Q4UNB2 (Rickettsia felis (strain ATCC VR-1525 / URRWXCal2))
Explore Q4UNB2 
Go to UniProtKB:  Q4UNB2
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ANTITOXIN OF TOXIN-ANTITOXIN SYSTEM VAPBEFGH78Rickettsia felisMutation(s): 0 
Find proteins for Q4UNB3 (Rickettsia felis (strain ATCC VR-1525 / URRWXCal2))
Explore Q4UNB3 
Go to UniProtKB:  Q4UNB3
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
DNAX26Rickettsia felis
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsLengthOrganismImage
DNAY26Rickettsia felis
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MES
Query on MES

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E, F, G, H
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.174 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.78α = 90
b = 92.333β = 90
c = 150.495γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-12-14
    Type: Initial release
  • Version 1.1: 2011-12-28
    Changes: Other
  • Version 1.2: 2012-04-25
    Changes: Other