Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans

Experimental Data Snapshot

  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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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: https://doi.org/10.1093/nar/gkx009
  • Primary Citation of Related Structures:  
    5GP9, 5GPA, 5GPC

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transcriptional regulator (TetR/AcrR family)
A, B
194Halalkalibacterium halodurans C-125Mutation(s): 0 
Gene Names: BH3102
Find proteins for Q9K8A4 (Halalkalibacterium halodurans (strain ATCC BAA-125 / DSM 18197 / FERM 7344 / JCM 9153 / C-125))
Explore Q9K8A4 
Go to UniProtKB:  Q9K8A4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9K8A4
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.873α = 90
b = 56.873β = 90
c = 200.884γ = 120
Software Package:
Software NamePurpose
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Research Foundation of Korea (NRF)Korea, Republic OfNRF; 2014R1A1A1A05008017
Agriculture Research CenterKorea, Republic OfARC; 710003-03
Global PhD FellowshipKorea, Republic OfNRF; 2011-0031110

Revision History  (Full details and data files)

  • Version 1.0: 2017-03-01
    Type: Initial release
  • Version 1.1: 2017-12-06
    Changes: Database references
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Derived calculations, Refinement description