3WHB

Crystal structure of FadR from Bacillus subtilis, a transcriptional regulator involved in the regulation of fatty acid degradation


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterization of a ligand-bound form of Bacillus subtilis FadR involved in the regulation of fatty acid degradation.

Fujihashi, M.Nakatani, T.Hirooka, K.Matsuoka, H.Fujita, Y.Miki, K.

(2014) Proteins 82: 1301-1310

  • DOI: 10.1002/prot.24496
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Bacillus subtilis FadR (FadR(Bs)), a member of the TetR family of bacterial transcriptional regulators, represses five fad operons including 15 genes, most of which are involved in β-oxidation of fatty acids. FadR(Bs) binds to the five FadR(Bs) boxes ...

    Bacillus subtilis FadR (FadR(Bs)), a member of the TetR family of bacterial transcriptional regulators, represses five fad operons including 15 genes, most of which are involved in β-oxidation of fatty acids. FadR(Bs) binds to the five FadR(Bs) boxes in the promoter regions and the binding is specifically inhibited by long-chain (C14-C20 ) acyl-CoAs, causing derepression of the fad operons. To elucidate the structural mechanism of this regulator, we have determined the crystal structures of FadR(Bs) proteins prepared with and without stearoyl(C18)-CoA. The crystal structure without adding any ligand molecules unexpectedly includes one small molecule, probably dodecyl(C12)-CoA derived from the Escherichia coli host, in its homodimeric structure. Also, we successfully obtained the structure of the ligand-bound form of the FadR(Bs) dimer by co-crystallization, in which two stearoyl-CoA molecules are accommodated, with the binding mode being essentially equivalent to that of dodecyl-CoA. Although the acyl-chain-binding cavity of FadR(Bs) is mainly hydrophobic, a hydrophilic patch encompasses the C1-C10 carbons of the acyl chain. This accounts for the previous report that the DNA binding of FadR(Bs) is specifically inhibited by the long-chain acyl-CoAs but not by the shorter ones. Structural comparison of the ligand-bound and unliganded subunits of FadR(Bs) revealed three regions around residues 21-31, 61-76, and 106-119 that were substantially changed in response to the ligand binding, and particularly with respect to the movements of Leu108 and Arg109. Site-directed mutagenesis of these residues revealed that Arg109, but not Leu108, is a key residue for maintenance of the DNA-binding affinity of FadR(Bs).


    Organizational Affiliation

    Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fatty acid metabolism regulator protein
A, B
194Bacillus subtilis (strain 168)Mutation(s): 0 
Gene Names: fadR (ysiA)
Find proteins for P94548 (Bacillus subtilis (strain 168))
Go to UniProtKB:  P94548
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DCC
Query on DCC

Download SDF File 
Download CCD File 
A
DODECYL-COA
C33 H58 N7 O17 P3 S
YMCXGHLSVALICC-GMHMEAMDSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.167α = 90.00
b = 66.105β = 90.00
c = 99.029γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
PDB_EXTRACTdata extraction
ADSCdata collection
HKL-2000data reduction
HKL-2000data scaling
SCALEPACKdata scaling
REFMACrefinement
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2017-02-22
    Type: Database references
  • Version 1.2: 2017-11-22
    Type: Refinement description