4ZED

PBP AccA from A. tumefaciens C58 in complex with agrocinopine-3'-O-benzoate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.174 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A Pyranose-2-Phosphate Motif Is Responsible for Both Antibiotic Import and Quorum-Sensing Regulation in Agrobacterium tumefaciens.

El Sahili, A.Li, S.Z.Lang, J.Virus, C.Planamente, S.Ahmar, M.Guimaraes, B.G.Aumont-Nicaise, M.Vigouroux, A.Soulere, L.Reader, J.Queneau, Y.Faure, D.Morera, S.

(2015) Plos Pathog. 11: e1005071-e1005071

  • DOI: 10.1371/journal.ppat.1005071
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefacie ...

    Periplasmic binding proteins (PBPs) in association with ABC transporters select and import a wide variety of ligands into bacterial cytoplasm. They can also take up toxic molecules, as observed in the case of the phytopathogen Agrobacterium tumefaciens strain C58. This organism contains a PBP called AccA that mediates the import of the antibiotic agrocin 84, as well as the opine agrocinopine A that acts as both a nutrient and a signalling molecule for the dissemination of virulence genes through quorum-sensing. Here, we characterized the binding mode of AccA using purified agrocin 84 and synthetic agrocinopine A by X-ray crystallography at very high resolution and performed affinity measurements. Structural and affinity analyses revealed that AccA recognizes an uncommon and specific motif, a pyranose-2-phosphate moiety which is present in both imported molecules via the L-arabinopyranose moiety in agrocinopine A and the D-glucopyranose moiety in agrocin 84. We hypothesized that AccA is a gateway allowing the import of any compound possessing a pyranose-2-phosphate motif at one end. This was structurally and functionally confirmed by experiments using four synthetic compounds: agrocinopine 3'-O-benzoate, L-arabinose-2-isopropylphosphate, L-arabinose-2-phosphate and D-glucose-2-phosphate. By combining affinity measurements and in vivo assays, we demonstrated that both L-arabinose-2-phosphate and D-glucose-2-phosphate, which are the AccF mediated degradation products of agrocinopine A and agrocin 84 respectively, interact with the master transcriptional regulator AccR and activate the quorum-sensing signal synthesis and Ti plasmid transfer in A. tumefaciens C58. Our findings shed light on the role of agrocinopine and antibiotic agrocin 84 on quorum-sensing regulation in A. tumefaciens and reveal how the PBP AccA acts as vehicle for the importation of both molecules by means of a key-recognition motif. It also opens future possibilities for the rational design of antibiotic and anti-virulence compounds against A. tumefaciens or other pathogens possessing similar PBPs.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), Department of Biophysics, Biochemistry and Structural Biology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France; Institute for Integrative Biology of the Cell (I2BC), Department of Microbiology, CNRS CEA University Paris-Sud, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter, substrate binding protein (Agrocinopines A and B)
A
499Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Gene Names: accA
Find proteins for Q7D2F4 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  Q7D2F4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
AGW
Query on AGW

Download SDF File 
Download CCD File 
A
[(2S,3S,4R,5R)-2,5-bis(hydroxymethyl)-2-[(2R,3R,4R,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-4-[oxidanyl-[(2R,3R,4S,5S)-2,4,5-tris(oxidanyl)oxan-3-yl]oxy-phosphoryl]oxy-oxolan-3-yl] benzoate
C24 H35 O19 P
LMASXRQPXQBKBC-GJRQBPJOSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.174 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 77.640α = 90.00
b = 114.920β = 90.00
c = 113.930γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XSCALEdata scaling
BUSTERrefinement
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-08-19
    Type: Initial release