Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 6.39 kDa 
• Atom Count: 390 
• Modelled Residue Count: 49 
• Deposited Residue Count: 55 
• Unique protein chains: 1

2L93

Solution structure of the C-terminal domain of Salmonella H-NS

• PDB DOI: 10.2210/pdb2L93/pdb
• BMRB: 17435

• Classification: DNA BINDING PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-29 Released: 2011-06-15 
• Deposition Author(s): Li, Y.

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Experimental Data Snapshot

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

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

• PubMed: 21673140 
• DOI: 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein H-NS	A	55	Salmonella enterica subsp. enterica serovar Typhimurium	Mutation(s): 0
UniProt
Find proteins for P0A1S2 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore P0A1S2  Go to UniProtKB:  P0A1S2

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2L93 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-01-29 
• Released Date: 2011-06-15 
Deposition Author(s): Li, Y.

Revision History  

• 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