5M3I | pdb_00005m3i

Macrodomain of Mycobacterium tuberculosis DarG

• PDB DOI: https://doi.org/10.2210/pdb5M3I/pdb

• Classification: ANTITOXIN
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-10-14 Released: 2016-12-21 
• Deposition Author(s): Ariza, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free: 
  0.251 (Depositor) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.214 (Depositor) 

Starting Model: experimental

Literature

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

• PubMed: 27939941 
• DOI: https://doi.org/10.1016/j.molcel.2016.11.014
• Primary Citation 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.

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Organizational Affiliation: 
• Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK.
Division for Marine and Environmental Research, Rudjer Boskovic Institute, Bijenicka cesta 54, 10000 Zagreb, Croatia.
Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE Oxford, UK. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.38 kDa 
• Atom Count: 4,789 
• Modeled Residue Count: 608 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RNase III inhibitor	A, B, C, D	165	Mycobacterium tuberculosis	Mutation(s): 0  EC: 3.2.2
UniProt
Find proteins for O53605 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore O53605  Go to UniProtKB:  O53605

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	E [auth A], F [auth B], G [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.17 Å
• R-Value Free:  0.251 (Depositor) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.214 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.84	α = 90
b = 75.45	β = 90
c = 116.12	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

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

Revision History  

• Version 1.0: 2016-12-21
  Type: Initial release
  
• Version 1.1: 2016-12-28
  Changes: Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Refinement description