6HQH

Structure of Agrobacterium tumefaciens B6 strain PBP SocA complexed with Deoxyfructosylglutamine (DFG) at 1.8 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Basis for High Specificity of Amadori Compound and Mannopine Opine Binding in Bacterial Pathogens.

Marty, L.Vigouroux, A.Aumont-Nicaise, M.Dessaux, Y.Faure, D.Morera, S.

(2016) J.Biol.Chem. 291: 22638-22649

  • DOI: 10.1074/jbc.M116.745562
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. Opines are either sugar phosphodiesters or the products of condensed amino acids with ketoacids or sugars. They are Agrobacteri ...

    Agrobacterium tumefaciens pathogens genetically modify their host plants to drive the synthesis of opines in plant tumors. Opines are either sugar phosphodiesters or the products of condensed amino acids with ketoacids or sugars. They are Agrobacterium nutrients and imported into the bacterial cell via periplasmic-binding proteins (PBPs) and ABC-transporters. Mannopine, an opine from the mannityl-opine family, is synthesized from an intermediate named deoxy-fructosyl-glutamine (DFG), which is also an opine and abundant Amadori compound (a name used for any derivative of aminodeoxysugars) present in decaying plant materials. The PBP MotA is responsible for mannopine import in mannopine-assimilating agrobacteria. In the nopaline-opine type agrobacteria strain, SocA protein was proposed as a putative mannopine binding PBP, and AttC protein was annotated as a mannopine binding-like PBP. Structural data on mannityl-opine-PBP complexes is currently lacking. By combining affinity data with analysis of seven x-ray structures at high resolution, we investigated the molecular basis of MotA, SocA, and AttC interactions with mannopine and its DFG precursor. Our work demonstrates that AttC is not a mannopine-binding protein and reveals a specific binding pocket for DFG in SocA with an affinity in nanomolar range. Hence, mannopine would not be imported into nopaline-type agrobacteria strains. In contrast, MotA binds both mannopine and DFG. We thus defined one mannopine and two DFG binding signatures. Unlike mannopine-PBPs, selective DFG-PBPs are present in a wide diversity of bacteria, including Actinobacteria, α-,β-, and γ-proteobacteria, revealing a common role of this Amadori compound in pathogenic, symbiotic, and opportunistic bacteria.


    Organizational Affiliation

    From the Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse, Gif-sur-Yvette 91198, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Membrane-bound lytic murein transglycosylase F
A
268Rhizobium radiobacterMutation(s): 0 
Find proteins for A0A0F4FYR3 (Rhizobium radiobacter)
Go to UniProtKB:  A0A0F4FYR3
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
EDO
Query on EDO

Download SDF File 
Download CCD File 
A
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
SNW
Query on SNW

Download SDF File 
Download CCD File 
A
Deoxyfructosylglutamine
santhopine
C11 H20 N2 O8
SNIATPDKUZZXAT-VISRLPHGSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 40.340α = 90.00
b = 63.690β = 104.81
c = 43.750γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
FFTphasing
XDSdata reduction
BUSTERrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2018-09-25 
  • Released Date: 2018-10-31 
  • Deposition Author(s): Morera, S., Marty, L.
  • This entry supersedes: 5L9M

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release
  • Version 1.1: 2019-05-15
    Type: Data collection, Database references