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 

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

  • 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 describ ...

    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.,Sect.D 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: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FATTY ACID METABOLISM REGULATOR PROTEIN
A, B
243Escherichia coli (strain K12)Gene Names: fadR (oleR, thdB)
Find proteins for P0A8V6 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A8V6
Entity ID: 2
MoleculeChainsLengthOrganism
5'-D(*CP*AP*TP*CP*TP*GP*GP*TP*AP*CP*GP*AP* CP*CP*AP*GP*AP*TP*C)-3'X19N/A
Entity ID: 3
MoleculeChainsLengthOrganism
5'-D(*GP*AP*TP*CP*TP*GP*GP*TP*CP*GP*TP*AP* CP*CP*AP*GP*AP*TP*G)-3'Y19N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download SDF File 
Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
AU
Query on AU

Download SDF File 
Download CCD File 
A, B
GOLD ION
Au
ZBKIUFWVEIBQRT-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DNAKd: 0.2 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.264 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 92.992α = 90.00
b = 92.992β = 90.00
c = 334.826γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
AMoREphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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