4JRI

Crystal Structure of Escherichia coli Hfq Proximal Edge Mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Mapping Hfq-RNA interaction surfaces using tryptophan fluorescence quenching.

Robinson, K.E.Orans, J.Kovach, A.R.Link, T.M.Brennan, R.G.

(2014) Nucleic Acids Res 42: 2736-2749

  • DOI: https://doi.org/10.1093/nar/gkt1171
  • Primary Citation of Related Structures:  
    4JLI, 4JRI, 4JRK, 4JUV

  • PubMed Abstract: 

    Hfq is a posttranscriptional riboregulator and RNA chaperone that binds small RNAs and target mRNAs to effect their annealing and message-specific regulation in response to environmental stressors. Structures of Hfq-RNA complexes indicate that U-rich sequences prefer the proximal face and A-rich sequences the distal face; however, the Hfq-binding sites of most RNAs are unknown. Here, we present an Hfq-RNA mapping approach that uses single tryptophan-substituted Hfq proteins, all of which retain the wild-type Hfq structure, and tryptophan fluorescence quenching (TFQ) by proximal RNA binding. TFQ properly identified the respective distal and proximal binding of A15 and U6 RNA to Gram-negative Escherichia coli (Ec) Hfq and the distal face binding of (AA)3A, (AU)3A and (AC)3A to Gram-positive Staphylococcus aureus (Sa) Hfq. The inability of (GU)3G to bind the distal face of Sa Hfq reveals the (R-L)n binding motif is a more restrictive (A-L)n binding motif. Remarkably Hfq from Gram-positive Listeria monocytogenes (Lm) binds (GU)3G on its proximal face. TFQ experiments also revealed the Ec Hfq (A-R-N)n distal face-binding motif should be redefined as an (A-A-N)n binding motif. TFQ data also demonstrated that the 5'-untranslated region of hfq mRNA binds both the proximal and distal faces of Ec Hfq and the unstructured C-terminus.


  • Organizational Affiliation

    Department of Biochemistry, Duke University, Durham, NC 27710, USA and Department of Biochemistry and Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein hfq
A, B, C, D
68Escherichia coli K-12Mutation(s): 1 
Gene Names: hfqb4172JW4130
UniProt
Find proteins for P0A6X3 (Escherichia coli (strain K12))
Explore P0A6X3 
Go to UniProtKB:  P0A6X3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6X3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.83 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.087α = 90
b = 90.087β = 90
c = 90.087γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2014-03-12
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references