2L92

Solution structure of the C-terminal domain of H-NS like protein Bv3F


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 basis for recognition of AT-rich DNA by unrelated xenogeneic silencing proteins

Gordon, B.R.G.Li, Y.Cote, A.Weirauch, M.T.Ding, P.Hughes, T.R.Navarre, W.W.Xia, B.Liu, J.

(2011) Proc Natl Acad Sci U S A 108: 10690-10695

  • DOI: https://doi.org/10.1073/pnas.1102544108
  • Primary Citation of Related Structures:  
    2L92, 2L93

  • PubMed Abstract: 

    H-NS and Lsr2 are nucleoid-associated proteins from Gram-negative bacteria and Mycobacteria, respectively, that play an important role in the silencing of horizontally acquired foreign DNA that is more AT-rich than the resident genome. Despite the fact that Lsr2 and H-NS proteins are dissimilar in sequence and structure, they serve apparently similar functions and can functionally complement one another. The mechanism by which these xenogeneic silencers selectively target AT-rich DNA has been enigmatic. We performed high-resolution protein binding microarray analysis to simultaneously assess the binding preference of H-NS and Lsr2 for all possible 8-base sequences. Concurrently, we performed a detailed structure-function relationship analysis of their C-terminal DNA binding domains by NMR. Unexpectedly, we found that H-NS and Lsr2 use a common DNA binding mechanism where a short loop containing a "Q/RGR" motif selectively interacts with the DNA minor groove, where the highest affinity is for AT-rich sequences that lack A-tracts. Mutations of the Q/RGR motif abolished DNA binding activity. Netropsin, a DNA minor groove-binding molecule effectively outcompeted H-NS and Lsr2 for binding to AT-rich sequences. These results provide a unified molecular mechanism to explain findings related to xenogeneic silencing proteins, including their lack of apparent sequence specificity but preference for AT-rich sequences. Our findings also suggest that structural information contained within the DNA minor groove is deciphered by xenogeneic silencing proteins to distinguish genetic material that is self from nonself.


  • Organizational Affiliation

    Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada M5S 1A8.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone family protein nucleoid-structuring protein H-NS50Burkholderia vietnamiensis G4Mutation(s): 0 
UniProt
Find proteins for A4JS72 (Burkholderia vietnamiensis (strain G4 / LMG 22486))
Explore A4JS72 
Go to UniProtKB:  A4JS72
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA4JS72
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

  • Released Date: 2011-06-15 
  • Deposition Author(s): Li, Y., Xia, B.

Revision History  (Full details and data files)

  • Version 1.0: 2011-06-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-28
    Changes: Database references
  • Version 1.3: 2023-02-08
    Changes: Data collection, Database references
  • Version 1.4: 2024-05-15
    Changes: Data collection, Database references