7OMY | pdb_00007omy

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

• PDB DOI: https://doi.org/10.2210/pdb7OMY/pdb
• NAKB: 7OMY

• Classification: TOXIN
• Organism(s): Thermus sp. 2.9
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2021-05-24 Released: 2021-06-23 
• Deposition Author(s): Schuller, M., Ariza, A.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.162 (Depositor) 

Starting Model: experimental

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

• PubMed: 34408320 
• DOI: https://doi.org/10.1038/s41586-021-03825-4
• Primary Citation 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.

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Organizational Affiliation: 
• Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
Biozentrum, University of Basel, Basel, Switzerland.
Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK.
Centre for Emerging, Endemic and Exotic Disease, Pathology and Population Sciences, The Royal Veterinary College, Hatfield, UK.
Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, UK. [e-mail].
Sir William Dunn School of Pathology, University of Oxford, Oxford, UK. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 26.84 kDa 
• Atom Count: 2,057 
• Modeled Residue Count: 214 
• Deposited Residue Count: 215 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DarT domain-containing protein	A [auth AAA]	210	Thermus sp. 2.9	Mutation(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 ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*TP*C)-3')	B [auth AeA]	5	Thermus sp. 2.9

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CNA (Subject of Investigation/LOI)	C [auth AAA]	CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE C22 H30 N7 O13 P2 DGPLSUKWXXSBCU-VGXGLJSLSA-O
GOL	E [auth AAA], F [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
SCN	D [auth AAA]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.197 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.162 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.499	α = 90
b = 39.104	β = 99.461
c = 61.636	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-06-23 
Deposition Author(s): Schuller, M., Ariza, A.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/R007195/1

Revision History  

• 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