7WNR | pdb_00007wnr

Data-driven HADDOCK model of mycobacterial nMazE6-operator DNA complex

• PDB DOI: https://doi.org/10.2210/pdb7WNR/pdb
• NAKB: 7WNR

• Classification: ANTITOXIN/DNA
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: chemical production metagenome, Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-01-19 Released: 2022-10-12 
• Deposition Author(s): Kumari, K., Sarma, S.P.
• Funding Organization(s): Department of Biotechnology (DBT, India)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 4 
• Selection Criteria: structures with favorable non-bond energy 

Literature

Structural and mutational analysis of MazE6-operator DNA complex provide insights into autoregulation of toxin-antitoxin systems.

Kumari, K., Sarma, S.P.

(2022) Commun Biol 5: 963-963

• PubMed: 36109664 
• DOI: https://doi.org/10.1038/s42003-022-03933-5
• Primary Citation Related Structures: 
  7WJ0, 7WNR


• PubMed Abstract: 
  

  Of the 10 paralogs of MazEF Toxin-Antitoxin system in Mycobacterium tuberculosis, MazEF6 plays an important role in multidrug tolerance, virulence, stress adaptation and Non Replicative Persistant (NRP) state establishment. The solution structures of the DNA binding domain of MazE6 and of its complex with the cognate operator DNA show that transcriptional regulation occurs by binding of MazE6 to an 18 bp operator sequence bearing the TANNNT motif (-10 region). Kinetics and thermodynamics of association, as determined by NMR and ITC, indicate that the nMazE6-DNA complex is of high affinity. Residues in N-terminal region of MazE6 that are key for its homodimerization, DNA binding specificity, and the base pairs in the operator DNA essential for the protein-DNA interaction, have been identified. It provides a basis for design of chemotherapeutic agents that will act via disruption of TA autoregulation, leading to cell death.

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Organizational Affiliation: 
• Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, Karnataka, 560012, India.
Molecular Biophysics Unit, Indian Institute of Science, C. V. Raman Road, Bangalore, Karnataka, 560012, India. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 22.72 kDa 
• Atom Count: 1,524 
• Modeled Residue Count: 134 
• Deposited Residue Count: 140 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antitoxin MazE6	C [auth B], D [auth C]	52	Mycobacterium tuberculosis H37Rv	Mutation(s): 0  Gene Names: mazE6, mazE-mt3, Rv1991A
UniProt
Find proteins for P9WJ87 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WJ87  Go to UniProtKB:  P9WJ87

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*CP*CP*GP*GP*TP*TP*AP*TP*AP*CP*TP*AP*TP*CP*TP*GP*TP*A)-3')	A	18	Mycobacterium tuberculosis H37Rv

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*AP*CP*AP*GP*AP*TP*AP*GP*TP*AP*TP*AP*AP*CP*CP*GP*G)-3')	B [auth D]	18	Mycobacterium tuberculosis H37Rv

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 4 
• Selection Criteria: structures with favorable non-bond energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-10-12 
Deposition Author(s): Kumari, K., Sarma, S.P.

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Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--

Revision History  

• Version 1.0: 2022-10-12
  Type: Initial release
  
• Version 1.1: 2024-05-15
  Changes: Data collection, Database references