2UXI

Phloretin in complex with TtgR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structures of Multidrug Binding Protein Ttgr in Complex with Antibiotics and Plant Antimicrobials.

Alguel, Y.Meng, C.Teran, W.Krell, T.Ramos, J.L.Gallegos, M.-T.Zhang, X.

(2007) J.Mol.Biol. 369: 829

  • DOI: 10.1016/j.jmb.2007.03.062
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibiotic resistance is a widely spread phenomenon. One major mechanism that underlies antibiotic resistance in bacteria is the active extrusion of toxic compounds through the membrane-bound efflux pumps that are often regulated at the transcription ...

    Antibiotic resistance is a widely spread phenomenon. One major mechanism that underlies antibiotic resistance in bacteria is the active extrusion of toxic compounds through the membrane-bound efflux pumps that are often regulated at the transcriptional level. TtgR represses the transcription of TtgABC, a key efflux pump in Pseudomonas putida, which is highly resistant to antibiotics, solvents and toxic plant secondary products. Previously we showed that TtgR is the only reported repressor that binds to different classes of natural antimicrobial compounds, which are also extruded by the efflux pump. We report here five high-resolution crystal structures of TtgR from the solvent-tolerant strain DOT-T1E, including TtgR in complex with common antibiotics and plant secondary metabolites. We provide structural basis for the unique ligand binding properties of TtgR. We identify two distinct and overlapping ligand binding sites; the first one is broader and consists of mainly hydrophobic residues, whereas the second one is deeper and contains more polar residues including Arg176, a unique residue present in the DOT-T1E strain but not in other Pseudomonas strains. Phloretin, a plant antimicrobial, can bind to both binding sites with distinct binding affinities and stoichiometries. Results on ligand binding properties of native and mutant TtgR proteins using isothermal titration calorimetry confirm the binding affinities and stoichiometries, and suggest a potential positive cooperativity between the two binding sites. The importance of Arg176 in phloretin binding was further confirmed by the reduced ability of phloretin in releasing the mutant TtgR from bound DNA compared to the native protein. The results presented here highlight the importance and versatility of regulatory systems in bacterial antibiotic resistance and open up new avenues for novel antimicrobial development.


    Organizational Affiliation

    Centre for Structural Biology and Division of Molecular Biosciences, Imperial College London, London, SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HTH-TYPE TRANSCRIPTIONAL REGULATOR TTGR
A, B
210Pseudomonas putida (strain DOT-T1E)Mutation(s): 0 
Gene Names: ttgR
Find proteins for Q9AIU0 (Pseudomonas putida (strain DOT-T1E))
Go to UniProtKB:  Q9AIU0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G50
Query on G50

Download SDF File 
Download CCD File 
A, B
3-(4-HYDROXYPHENYL)-1-(2,4,6-TRIHYDROXYPHENYL)PROPAN-1-ONE
C15 H14 O5
VGEREEWJJVICBM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
G50ΔG: -26.5 - -42.6 kJ/mol (100) BINDINGDB
G50Kd: 50 nM BINDINGMOAD
G50Kd: 50 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.245 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 47.221α = 90.00
b = 230.614β = 90.00
c = 43.942γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance