5ITO

Structure of the periplasmic binding protein M117N-NocT from A. tumefaciens in complex with octopine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1038/ismej.2016.137
  • Primary Citation of Related Structures:  
    5ITO, 5ITP

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Nopaline-binding periplasmic protein
A, B
265Agrobacterium fabrum str. C58Mutation(s): 0 
Gene Names: nocTAtu6027AGR_pTi_67
UniProt
Find proteins for P35120 (Agrobacterium fabrum (strain C58 / ATCC 33970))
Explore P35120 
Go to UniProtKB:  P35120
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35120
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6DB
Query on 6DB

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B]
octopine
C9 H18 N4 O4
IMXSCCDUAFEIOE-RITPCOANSA-N
1PE
Query on 1PE

Download Ideal Coordinates CCD File 
E [auth A]PENTAETHYLENE GLYCOL
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
TOE
Query on TOE

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A]
2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXYL
C7 H16 O4
JLGLQAWTXXGVEM-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
C [auth A]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
D [auth A],
I [auth B],
J [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.177 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.59α = 90
b = 113.59β = 90
c = 37.89γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFrance--

Revision History  (Full details and data files)

  • Version 1.0: 2016-11-30
    Type: Initial release
  • Version 1.1: 2017-02-01
    Changes: Database references
  • Version 1.2: 2017-09-06
    Changes: Author supporting evidence
  • Version 1.3: 2024-01-10
    Changes: Data collection, Database references, Refinement description