5ITP

Structure of the periplasmic binding protein NocT from A.tumefaciens in complex with octopine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Fitness costs restrict niche expansion by generalist niche-constructing pathogens.

Lang, J.Vigouroux, A.El Sahili, A.Kwasiborski, A.Aumont-Nicaise, M.Dessaux, Y.Shykoff, J.A.Morera, S.Faure, D.

(2017) ISME J 11: 374-385

  • DOI: 10.1038/ismej.2016.137
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant ...

    We investigated the molecular and ecological mechanisms involved in niche expansion, or generalism, versus specialization in sympatric plant pathogens. Nopaline-type and octopine-type Agrobacterium tumefaciens engineer distinct niches in their plant hosts that provide different nutrients: nopaline or octopine, respectively. Previous studies revealed that nopaline-type pathogens may expand their niche to also assimilate octopine in the presence of nopaline, but consequences of this phenomenon on pathogen dynamics in planta were not known. Here, we provided molecular insight into how the transport protein NocT can bind octopine as well as nopaline, contributing to niche expansion. We further showed that despite the ability for niche expansion, nopaline-type pathogens had no competitive advantage over octopine-type pathogens in co-infected plants. We also demonstrated that a single nucleotide polymorphism in the nocR gene was sufficient to allow octopine assimilation by nopaline-type strains even in absence of nopaline. The evolved nocR bacteria had higher fitness than their ancestor in octopine-rich transgenic plants but lower fitness in tumors induced by octopine-type pathogens. Overall, this work elucidates the specialization of A. tumefaciens to particular opine niches and explains why generalists do not always spread despite the advantage associated with broader nutritional niches.


    Organizational Affiliation

    Institute for Integrative Biology of the Cell (I2BC), CNRS CEA Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Nopaline-binding periplasmic protein
A, B
265Agrobacterium fabrum (strain C58 / ATCC 33970)Mutation(s): 0 
Gene Names: nocT
Find proteins for P35120 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Go to UniProtKB:  P35120
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6DB
Query on 6DB

Download SDF File 
Download CCD File 
A, B
octopine
C9 H18 N4 O4
IMXSCCDUAFEIOE-RITPCOANSA-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
PEG
Query on PEG

Download SDF File 
Download CCD File 
A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6DBKd: 6100 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.177 
  • Space Group: P 32
Unit Cell:
Length (Å)Angle (°)
a = 114.640α = 90.00
b = 114.640β = 90.00
c = 38.080γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History 

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-02-01
    Type: Database references
  • Version 2.0: 2017-09-06
    Type: Atomic model, Author supporting evidence