2K29

Structure of the DBD domain of E. coli antitoxin RelB


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural mechanism of transcriptional autorepression of the Escherichia coli RelB/RelE antitoxin/toxin module.

Li, G.Y.Zhang, Y.Inouye, M.Ikura, M.

(2008) J Mol Biol 380: 107-119

  • DOI: https://doi.org/10.1016/j.jmb.2008.04.039
  • Primary Citation of Related Structures:  
    2K29

  • PubMed Abstract: 

    The Escherichia coli chromosomal relBE operon encodes a toxin-antitoxin system, which is autoregulated by its protein products, RelB and RelE. RelB acts as a transcriptional repressor and RelE functions as a cofactor to enhance the repressor activity of RelB. Here, we present the NMR-derived structure of a RelB dimer and show that a RelB dimer recognizes a hexad repeat in the palindromic operator region through a ribbon-helix-helix motif. Our biochemical data show that two weakly associated RelB dimers bind to the adjacent repeats in the 3'-site of the operator (O(R)) at a moderate affinity (K(d), approximately 10(-5) M). However, in the presence of RelE, a RelB tetramer binds two distinct binding sites within the operator region, each with an enhanced affinity (K(d), approximately 10(-6) M for the low-affinity site, O(L), and 10(-8) M for the high-affinity site, O(R)). We propose that the enhanced affinity for the operator element is mediated by a cooperative DNA binding by a pair of RelB dimers and that the interaction between RelB dimers is strongly augmented by the presence of the cognate toxin RelE.


  • Organizational Affiliation

    Division of Signaling Biology, Ontario Cancer Institute and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Antitoxin RelB
A, B
53Escherichia coliMutation(s): 0 
Gene Names: relB
UniProt
Find proteins for P0C079 (Escherichia coli (strain K12))
Explore P0C079 
Go to UniProtKB:  P0C079
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0C079
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2020-02-19
    Changes: Database references, Derived calculations, Other
  • Version 1.3: 2023-06-14
    Changes: Database references, Other
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references