6D0I

ParT: Prs ADP-ribosylating toxin bound to cognate antitoxin ParS. L48M ParT, SeMet-substituted complex.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.159 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

ParST is a widespread toxin-antitoxin module that targets nucleotide metabolism.

Piscotta, F.J.Jeffrey, P.D.Link, A.J.

(2018) Proc. Natl. Acad. Sci. U.S.A. --: --

  • DOI: 10.1073/pnas.1814633116
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Toxin-antitoxin (TA) systems interfere with essential cellular processes and are implicated in bacterial lifestyle adaptations such as persistence and the biofilm formation. Here, we present structural, biochemical, and functional data on an uncharac ...

    Toxin-antitoxin (TA) systems interfere with essential cellular processes and are implicated in bacterial lifestyle adaptations such as persistence and the biofilm formation. Here, we present structural, biochemical, and functional data on an uncharacterized TA system, the COG5654-COG5642 pair. Bioinformatic analysis showed that this TA pair is found in 2,942 of the 16,286 distinct bacterial species in the RefSeq database. We solved a structure of the toxin bound to a fragment of the antitoxin to 1.50 Å. This structure suggested that the toxin is a mono-ADP-ribosyltransferase (mART). The toxin specifically modifies phosphoribosyl pyrophosphate synthetase (Prs), an essential enzyme in nucleotide biosynthesis conserved in all organisms. We propose renaming the toxin ParT for Prs ADP-ribosylating toxin and ParS for the cognate antitoxin. ParT is a unique example of an intracellular protein mART in bacteria and is the smallest known mART. This work demonstrates that TA systems can induce bacteriostasis through interference with nucleotide biosynthesis.


    Organizational Affiliation

    Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ParT: COG5654 (RES domain) toxin
A, C
160Sphingobium sp. YBL2Mutation(s): 1 
Find proteins for A0A0C5XL88 (Sphingobium sp. YBL2)
Go to UniProtKB:  A0A0C5XL88
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ParS: COG5642 (DUF2384) antitoxin fragment
B, D
72Sphingobium sp. YBL2Mutation(s): 0 
Find proteins for A0A0C5XKJ0 (Sphingobium sp. YBL2)
Go to UniProtKB:  A0A0C5XKJ0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
C
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.159 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 41.977α = 84.68
b = 51.319β = 73.82
c = 57.941γ = 85.51
Software Package:
Software NamePurpose
PHENIXrefinement
MERLOTphasing
PDB_EXTRACTdata extraction
Aimlessdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-01-09
    Type: Initial release