6GW7

The CTD of HpDprA, a DNA binding Winged Helix domain which do not bind dsDNA


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

The C-terminal domain of HpDprA is a DNA-binding winged helix domain that does not bind double-stranded DNA.

Lisboa, J.Celma, L.Sanchez, D.Marquis, M.Andreani, J.Guerois, R.Ochsenbein, F.Durand, D.Marsin, S.Cuniasse, P.Radicella, J.P.Quevillon-Cheruel, S.

(2019) FEBS J 286: 1941-1958

  • DOI: https://doi.org/10.1111/febs.14788
  • Primary Citation of Related Structures:  
    5MLL, 6GW7

  • PubMed Abstract: 

    DNA-processing protein A, a ubiquitous multidomain DNA-binding protein, plays a crucial role during natural transformation in bacteria. Here, we carried out the structural analysis of DprA from the human pathogen Helicobacter pylori by combining data issued from the 1.8-Å resolution X-ray structure of the Pfam02481 domain dimer (RF), the NMR structure of the carboxy terminal domain (CTD), and the low-resolution structure of the full-length DprA dimer obtained in solution by SAXS. In particular, we sought a molecular function for the CTD, a domain that we show here is essential for transformation in H. pylori. Albeit its structural homology to winged helix DNA-binding motifs, we confirmed that the isolated CTD does not interact with ssDNA nor with dsDNA. The key R52 and K137 residues of RF are crucial for these two interactions. Search for sequences harboring homology to either HpDprA or Rhodopseudomonas palustris DprA CTDs led to the identification of conserved patches in the two CTD. Our structural study revealed the similarity of the structures adopted by these residues in RpDprA CTD and HpDprA CTD. This argues for a conserved, but yet to be defined, CTD function, distinct from DNA binding.


  • Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Gif-sur-Yvette, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA protecting protein DprA59Helicobacter pyloriMutation(s): 0 
Gene Names: BB415_01075
UniProt
Find proteins for A0A2A6XLY0 (Helicobacter pylori)
Explore A0A2A6XLY0 
Go to UniProtKB:  A0A2A6XLY0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2A6XLY0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 80 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceANR-10-INSB-05-01
French National Research AgencyFranceANR-IAB-2011
French National Research AgencyFranceANR-10-BLAN-1328

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-08
    Changes: Data collection
  • Version 1.2: 2019-05-29
    Changes: Data collection, Database references
  • Version 1.3: 2020-11-18
    Changes: Data collection, Refinement description
  • Version 1.4: 2023-06-14
    Changes: Database references, Other