Macrodomain of Thermus aquaticus DarG

Experimental Data Snapshot

  • Resolution: 1.67 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

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This is version 1.3 of the entry. See complete history


The Toxin-Antitoxin System DarTG Catalyzes Reversible ADP-Ribosylation of DNA.

Jankevicius, G.Ariza, A.Ahel, M.Ahel, I.

(2016) Mol Cell 64: 1109-1116

  • DOI: https://doi.org/10.1016/j.molcel.2016.11.014
  • Primary Citation of Related Structures:  
    5M31, 5M3E, 5M3I

  • PubMed Abstract: 

    The discovery and study of toxin-antitoxin (TA) systems helps us advance our understanding of the strategies prokaryotes employ to regulate cellular processes related to the general stress response, such as defense against phages, growth control, biofilm formation, persistence, and programmed cell death. Here we identify and characterize a TA system found in various bacteria, including the global pathogen Mycobacterium tuberculosis. The toxin of the system (DarT) is a domain of unknown function (DUF) 4433, and the antitoxin (DarG) a macrodomain protein. We demonstrate that DarT is an enzyme that specifically modifies thymidines on single-stranded DNA in a sequence-specific manner by a nucleotide-type modification called ADP-ribosylation. We also show that this modification can be removed by DarG. Our results provide an example of reversible DNA ADP-ribosylation, and we anticipate potential therapeutic benefits by targeting this enzyme-enzyme TA system in bacterial pathogens such as M. tuberculosis.

  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Appr-1-p processing domain protein165Thermus aquaticus Y51MC23Mutation(s): 0 
Gene Names: TaqDRAFT_4250
Find proteins for P0DV57 (Thermus aquaticus (strain ATCC BAA-2747 / Y51MC23))
Explore P0DV57 
Go to UniProtKB:  P0DV57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DV57
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.67 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.6α = 90
b = 45.02β = 101.25
c = 35.54γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

  • Released Date: 2016-12-21 
  • Deposition Author(s): Ariza, A.

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-21
    Type: Initial release
  • Version 1.1: 2016-12-28
    Changes: Database references
  • Version 1.2: 2018-03-07
    Changes: Source and taxonomy
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description