5GPC

Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of operator sites recognition and effector binding in the TetR family transcription regulator FadR.

Yeo, H.K.Park, Y.W.Lee, J.Y.

(2017) Nucleic Acids Res. 45: 4244-4254

  • DOI: 10.1093/nar/gkx009
  • Primary Citation of Related Structures:  5GP9, 5GPA

  • PubMed Abstract: 
  • FadR is a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. In this study, the crystal structures of Bacillus halodurans FadR, which belong to the TetR fami ...

    FadR is a fatty acyl-CoA dependent transcription factor that regulates genes encoding proteins involved in fatty-acid degradation and synthesis pathways. In this study, the crystal structures of Bacillus halodurans FadR, which belong to the TetR family, have been determined in three different forms: ligand-bound, ligand-free and DNA-bound at resolutions of 1.75, 2.05 and 2.80 Å, respectively. Structural and functional data showed that B. halodurans FadR was bound to its operator site without fatty acyl-CoAs. Structural comparisons among the three different forms of B. halodurans FadR revealed that the movement of DNA binding domains toward the operator DNA was blocked upon binding of ligand molecules. These findings suggest that the TetR family FadR negatively regulates the genes involved in fatty acid metabolism by binding cooperatively to the operator DNA as a dimer of dimers.


    Organizational Affiliation

    Department of Life Science, Dongguk University-Seoul, 32, Dongguk-ro, Ilsandong-gu, Goyang, Gyeonggi-do 10326, Republic of Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Transcriptional regulator (TetR/AcrR family)
A, B, C, D
194Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125)N/A
Find proteins for Q9K8A4 (Bacillus halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Go to UniProtKB:  Q9K8A4
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(P*CP*AP*TP*GP*AP*AP*TP*GP*AP*GP*TP*AP*TP*TP*CP*AP*TP*TP*CP*AP*T)-3')G21synthetic construct
Entity ID: 3
MoleculeChainsLengthOrganism
DNA (5'-D(P*GP*AP*TP*GP*AP*AP*TP*GP*AP*AP*TP*AP*CP*TP*CP*AP*TP*TP*CP*AP*T)-3')E21synthetic construct
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.205 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 46.500α = 103.83
b = 76.935β = 105.48
c = 87.022γ = 89.64
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Research Foundation of KoreaKorea, Republic OfNRF; 2014R1A1A1A05008017
Agriculture Research CenterKorea, Republic OfARC; 710003-03
Global PhD Fellowship programKorea, Republic OfNRF-2011-0031110

Revision History 

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Type: Database references