1H9T

FADR, FATTY ACID RESPONSIVE TRANSCRIPTION FACTOR FROM E. COLI IN COMPLEX WITH FADB OPERATOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.264 
  • R-Value Observed: 0.265 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The Structural Basis of Acyl Coenzyme A-Dependent Regulation of the Transcription Factor Fadr

Van Aalten, D.M.F.Dirusso, C.C.Knudsen, J.

(2001) EMBO J 20: 2041

  • DOI: 10.1093/emboj/20.8.2041
  • Primary Citation of Related Structures:  
    1H9G, 1H9T

  • PubMed Abstract: 
  • FadR is an acyl-CoA-responsive transcription factor, regulating fatty acid biosynthetic and degradation genes in Escherichia coli. The apo-protein binds DNA as a homodimer, an interaction that is disrupted by binding of acyl-COA: The recently described structure of apo-FadR shows a DNA binding domain coupled to an acyl-CoA binding domain with a novel fold, but does not explain how binding of the acyl-CoA effector molecule > 30 A away from the DNA binding site affects transcriptional regulation ...

    FadR is an acyl-CoA-responsive transcription factor, regulating fatty acid biosynthetic and degradation genes in Escherichia coli. The apo-protein binds DNA as a homodimer, an interaction that is disrupted by binding of acyl-COA: The recently described structure of apo-FadR shows a DNA binding domain coupled to an acyl-CoA binding domain with a novel fold, but does not explain how binding of the acyl-CoA effector molecule > 30 A away from the DNA binding site affects transcriptional regulation. Here, we describe the structures of the FadR-operator and FadR- myristoyl-CoA binary complexes. The FadR-DNA complex reveals a novel winged helix-turn-helix protein-DNA interaction, involving sequence-specific contacts from the wing to the minor groove. Binding of acyl-CoA results in dramatic conformational changes throughout the protein, with backbone shifts up to 4.5 A. The net effect is a rearrangement of the DNA binding domains in the dimer, resulting in a change of 7.2 A in separation of the DNA recognition helices and the loss of DNA binding, revealing the molecular basis of acyl-CoA-responsive regulation.


    Related Citations: 
    • Crystal Structure of Fadr, a Fatty Acid-Responsive Transcription Factor with a Novel Acyl Coenzyme A-Binding Fold
      Van Aalten, D.M., Dirusso, C.C., Knudsen, J., Wierenga, R.K.
      (2000) EMBO J 19: 5167
    • Crystallization and X-Ray Diffraction Studies of the Fatty-Acid Responsive Transcription Factor Fadr from Escherichia Coli
      Van Aalten, D.M.F., Knudsen, J., Dirusso, C.C., Kokko, T., Wierenga, R.K.
      (2000) Acta Crystallogr D Biol Crystallogr 56: 469

    Organizational Affiliation

    Wellcome Trust Biocentre, Division of Biological Chemistry and Molecular Microbiology, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK. dava@davapc1.bioch.dundee.ac.uk



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FATTY ACID METABOLISM REGULATOR PROTEINA, B243Escherichia coliMutation(s): 0 
UniProt
Find proteins for P0A8V6 (Escherichia coli (strain K12))
Explore P0A8V6 
Go to UniProtKB:  P0A8V6
Protein Feature View
Expand
  • Reference Sequence
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 2
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*AP*TP*CP*TP*GP*GP*TP*AP*CP*GP*AP* CP*CP*AP*GP*AP*TP*C)-3'C [auth X]19N/A
    Protein Feature View
    Expand
    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 3
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*AP*TP*CP*TP*GP*GP*TP*CP*GP*TP*AP* CP*CP*AP*GP*AP*TP*G)-3'D [auth Y]19N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Small Molecules
      Binding Affinity Annotations 
      IDSourceBinding Affinity
      DNA PDBBind:  1H9T Kd: 0.2 (nM) from 1 assay(s)
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 3.25 Å
      • R-Value Free: 0.320 
      • R-Value Work: 0.264 
      • R-Value Observed: 0.265 
      • Space Group: P 61 2 2
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 92.992α = 90
      b = 92.992β = 90
      c = 334.826γ = 120
      Software Package:
      Software NamePurpose
      REFMACrefinement
      DENZOdata reduction
      SCALEPACKdata scaling
      AMoREphasing

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2001-04-04
        Type: Initial release
      • Version 1.1: 2011-05-07
        Changes: Version format compliance
      • Version 1.2: 2011-07-13
        Changes: Version format compliance