4PDK

FadR, Fatty Acid Responsive Transcription Factor from Vibrio cholerae, in Complex with oleoyl-CoA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.263 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

The 40-residue insertion in Vibrio cholerae FadR facilitates binding of an additional fatty acyl-CoA ligand.

Shi, W.Kovacikova, G.Lin, W.Taylor, R.K.Skorupski, K.Kull, F.J.

(2015) Nat Commun 6: 6032-6032

  • DOI: 10.1038/ncomms7032
  • Primary Citation of Related Structures:  
    4P96, 4P9U, 4PDK

  • PubMed Abstract: 
  • FadR is a master regulator of fatty acid metabolism and influences virulence in certain members of Vibrionaceae. Among FadR homologues of the GntR family, the Vibrionaceae protein is unusual in that it contains a C-terminal 40-residue insertion. Here we report the structure of Vibrio cholerae FadR (VcFadR) alone, bound to DNA, and in the presence of a ligand, oleoyl-CoA ...

    FadR is a master regulator of fatty acid metabolism and influences virulence in certain members of Vibrionaceae. Among FadR homologues of the GntR family, the Vibrionaceae protein is unusual in that it contains a C-terminal 40-residue insertion. Here we report the structure of Vibrio cholerae FadR (VcFadR) alone, bound to DNA, and in the presence of a ligand, oleoyl-CoA. Whereas Escherichia coli FadR (EcFadR) contains only one acyl-CoA-binding site in each monomer, crystallographic and calorimetric data indicate that VcFadR has two. One of the binding sites resembles that of EcFadR, whereas the other, comprised residues from the insertion, has not previously been observed. Upon ligand binding, VcFadR undergoes a dramatic conformational change that would more fully disrupt DNA binding than EcFadR. These findings suggest that the ability to bind and respond to an additional ligand allows FadR from Vibrionaceae to function as a more efficient regulator.


    Organizational Affiliation

    1] Department of Biochemistry, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire 03755, USA [2] Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fatty acid metabolism regulator proteinA, B279Vibrio cholerae O1 biovar El Tor str. N16961Mutation(s): 0 
Gene Names: fadRVC_1900
UniProt
Find proteins for Q9KQU8 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961))
Explore Q9KQU8 
Go to UniProtKB:  Q9KQU8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9KQU8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3VV
Query on 3VV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth B],
F [auth B]
S-{(3R,5R,9R)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8-dimethyl-3,5-dioxido-10,14-dioxo-2,4,6-trioxa-11,15-diaza-3lambda~5~,5lambda~5~-diphosphaheptadecan-17-yl} (9Z)-octadec-9-enethioate (non-preferred name)
C39 H68 N7 O17 P3 S
XDUHQPOXLUAVEE-BPMMELMSSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.298 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.263 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 116.92α = 90
b = 88.69β = 90
c = 62.86γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI072661

Revision History  (Full details and data files)

  • Version 1.0: 2015-02-18
    Type: Initial release
  • Version 1.1: 2015-02-25
    Changes: Derived calculations
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Derived calculations, Refinement description, Source and taxonomy
  • Version 1.3: 2019-12-11
    Changes: Author supporting evidence