6IFM

Crystal structure of DNA bound VapBC from Salmonella typhimurium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Crystal structure of proteolyzed VapBC and DNA-bound VapBC from Salmonella enterica Typhimurium LT2 and VapC as a putative Ca2+-dependent ribonuclease.

Park, D.Yoon, H.J.Lee, K.Y.Park, S.J.Cheon, S.H.Lee, H.H.Lee, S.J.Lee, B.J.

(2019) Faseb J. --: --

  • DOI: 10.1096/fj.201901989R
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacterial toxin-antitoxin (TA) system has gained attention for its essential roles in cellular maintenance and survival under harsh environmental conditions such as nutrient deficiency and antibiotic treatment. There are at least 14 TA systems in Sal ...

    Bacterial toxin-antitoxin (TA) system has gained attention for its essential roles in cellular maintenance and survival under harsh environmental conditions such as nutrient deficiency and antibiotic treatment. There are at least 14 TA systems in Salmonella enterica serovar Typhimurium LT2, a pathogenic bacterium, and none of the structures of these TA systems have been determined. We determined the crystal structure of the VapBC TA complex from S. Typhimurium LT2 in proteolyzed and DNA-bound forms at 2.0 Å and 2.8 Å resolution, respectively. The VapC toxin possesses a pilT N-terminal domain (PIN-domain) that shows ribonuclease activity, and the VapB antitoxin has an AbrB-type DNA binding domain. In addition, the structure revealed details of interaction mode between VapBC and the cognate promoter DNA, including the inhibition of VapC by VapB and linear conformation of bound DNA in the VapBC complex. The complexation of VapBC with the linear DNA is not consistent with known structures of VapBC homologs in complex with bent DNA. We also identified VapC from S. Typhimurium LT2 as a putative Ca 2+ -dependent ribonuclease, which differs from previous data showing that VapC homologs have Mg 2+ or Mn 2+ -dependent ribonuclease activities. The present studies could provide structural understanding of the physiology of VapBC systems and foundation for the development of new antibiotic drugs against Salmonella infection.


    Organizational Affiliation

    Pohang Accelerator Laboratory, Pohang University of Science and Technology, Pohang, Korea.,Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul, Republic of Korea.,College of Pharmacy, Gachon University, Incheon, Republic of Korea.,The Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Department of Medical Biophysics, University of Toronto, Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
tRNA(fMet)-specific endonuclease VapC
A, E, C, G
132Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: vapC
EC: 3.1.-.-
Find proteins for Q8ZM86 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q8ZM86
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antitoxin VapB
B, F, H, D
68Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)Mutation(s): 0 
Gene Names: vapB
Find proteins for Q7CPV2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720))
Go to UniProtKB:  Q7CPV2
Entity ID: 3
MoleculeChainsLengthOrganism
DNA forward (27-MER)M27synthetic construct
Entity ID: 4
MoleculeChainsLengthOrganism
DNA backward (27-MER)N27synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.804 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.206 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 93.677α = 90.00
b = 93.677β = 90.00
c = 122.440γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-09-20 
  • Released Date: 2020-01-29 
  • Deposition Author(s): Park, D.W., Lee, B.J.

Funding OrganizationLocationGrant Number
National Research Foundation (Korea)Korea, Republic Of2018R1A2A1A19018526
National Research Foundation (Korea)Korea, Republic Of2018R1A5A2024425

Revision History 

  • Version 1.0: 2020-01-29
    Type: Initial release