7OMX

Thermus sp. 2.9 DarT in complex with carba-NAD+


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work: 
    0.173 (Depositor), 0.180 (DCC) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Molecular basis for DarT ADP-ribosylation of a DNA base.

Schuller, M.Butler, R.E.Ariza, A.Tromans-Coia, C.Jankevicius, G.Claridge, T.D.W.Kendall, S.L.Goh, S.Stewart, G.R.Ahel, I.

(2021) Nature 596: 597-602

  • DOI: https://doi.org/10.1038/s41586-021-03825-4
  • Primary Citation of Related Structures:  
    7OMU, 7OMV, 7OMW, 7OMX, 7OMY, 7OMZ, 7ON0

  • PubMed Abstract: 

    ADP-ribosyltransferases use NAD + to catalyse substrate ADP-ribosylation 1 , and thereby regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria 2-4 . Reversible ADP-ribosylation has traditionally been considered a protein-specific modification 5 , but recent in vitro studies have suggested nucleic acids as targets 6-9 . Here we present evidence that specific, reversible ADP-ribosylation of DNA on thymidine bases occurs in cellulo through the DarT-DarG toxin-antitoxin system, which is found in a variety of bacteria (including global pathogens such as Mycobacterium tuberculosis, enteropathogenic Escherichia coli and Pseudomonas aeruginosa) 10 . We report the structure of DarT, which identifies this protein as a diverged member of the PARP family. We provide a set of high-resolution structures of this enzyme in ligand-free and pre- and post-reaction states, which reveals a specialized mechanism of catalysis that includes a key active-site arginine that extends the canonical ADP-ribosyltransferase toolkit. Comparison with PARP-HPF1, a well-established DNA repair protein ADP-ribosylation complex, offers insights into how the DarT class of ADP-ribosyltransferases evolved into specific DNA-modifying enzymes. Together, our structural and mechanistic data provide details of this PARP family member and contribute to a fundamental understanding of the ADP-ribosylation of nucleic acids. We also show that thymine-linked ADP-ribose DNA adducts reversed by DarG antitoxin (functioning as a noncanonical DNA repair factor) are used not only for targeted DNA damage to induce toxicity, but also as a signalling strategy for cellular processes. Using M. tuberculosis as an exemplar, we show that DarT-DarG regulates growth by ADP-ribosylation of DNA at the origin of chromosome replication.


  • Organizational Affiliation

    Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DarT domain-containing proteinA [auth AAA]210Thermus sp. 2.9Mutation(s): 1 
Gene Names: QT17_01930
EC: 2.4.2
UniProt
Find proteins for A0A0B0SG80 (Thermus sp. (strain 2.9))
Explore A0A0B0SG80 
Go to UniProtKB:  A0A0B0SG80
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B0SG80
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.203 (Depositor), 0.210 (DCC) 
  • R-Value Work:  0.173 (Depositor), 0.180 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.034α = 90
b = 71.282β = 90
c = 85.542γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted CNAClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/R007195/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-23
    Type: Initial release
  • Version 2.0: 2021-10-13
    Changes: Atomic model, Data collection, Database references
  • Version 2.1: 2024-05-01
    Changes: Data collection, Derived calculations, Refinement description