Solution structure of the bacterial antidote ParD

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 24 
  • Selection Criteria: structures with the lowest energy 

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This is version 1.4 of the entry. See complete history


The solution structure of ParD, the antidote of the ParDE toxin antitoxin module, provides the structural basis for DNA and toxin binding.

Oberer, M.Zangger, K.Gruber, K.Keller, W.

(2007) Protein Sci 16: 1676-1688

  • DOI: https://doi.org/10.1110/ps.062680707
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    ParD is the antidote of the plasmid-encoded toxin-antitoxin (TA) system ParD-ParE. These modules rely on differential stabilities of a highly expressed but labile antidote and a stable toxin expressed from one operon. Consequently, loss of the coding plasmid results in loss of the protective antidote and poisoning of the cell. The antidote protein usually also exhibits an autoregulatory function of the operon. In this paper, we present the solution structure of ParD. The repressor activity of ParD is mediated by the N-terminal half of the protein, which adopts a ribbon-helix-helix (RHH) fold. The C-terminal half of the protein is unstructured in the absence of its cognate binding partner ParE. Based on homology with other RHH proteins, we present a model of the ParD-DNA interaction, with the antiparallel beta-strand being inserted into the major groove of DNA. The fusion of the N-terminal DNA-binding RHH motif to the toxin-binding unstructured C-terminal domain is discussed in its evolutionary context.

  • Organizational Affiliation

    Institut für Chemie, Arbeitsgruppe Strukturbiologie, Karl-Franzens-Universität Graz, A-8010 Graz, Austria.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein parD
A, B
83Escherichia coliMutation(s): 0 
Find proteins for P22995 (Escherichia coli)
Explore P22995 
Go to UniProtKB:  P22995
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22995
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 150 
  • Conformers Submitted: 24 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-09-05
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2020-02-26
    Changes: Data collection, Database references, Derived calculations, Other
  • Version 1.4: 2023-06-14
    Changes: Database references, Other