5GP9

Structural analysis of fatty acid degradation regulator FadR from Bacillus halodurans


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

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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, 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 ...

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Transcriptional regulator (TetR/AcrR family)A, B194Alkalihalobacillus halodurans C-125Mutation(s): 0 
Gene Names: BH3102
UniProt
Find proteins for Q9K8A4 (Alkalihalobacillus 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PLM
Query on PLM

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
C [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • 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
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

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