4PP0

Structure of the PBP NocT-M117N in complex with pyronopaline


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Agrobacterium uses a unique ligand-binding mode for trapping opines and acquiring a competitive advantage in the niche construction on plant host.

Lang, J.Vigouroux, A.Planamente, S.El Sahili, A.Blin, P.Aumont-Nicaise, M.Dessaux, Y.Morera, S.Faure, D.

(2014) PLoS Pathog 10: e1004444-e1004444

  • DOI: https://doi.org/10.1371/journal.ppat.1004444
  • Primary Citation of Related Structures:  
    4P0I, 4POW, 4PP0, 5OVZ

  • PubMed Abstract: 

    By modifying the nuclear genome of its host, the plant pathogen Agrobacterium tumefaciens induces the development of plant tumours in which it proliferates. The transformed plant tissues accumulate uncommon low molecular weight compounds called opines that are growth substrates for A. tumefaciens. In the pathogen-induced niche (the plant tumour), a selective advantage conferred by opine assimilation has been hypothesized, but not experimentally demonstrated. Here, using genetics and structural biology, we deciphered how the pathogen is able to bind opines and use them to efficiently compete in the plant tumour. We report high resolution X-ray structures of the periplasmic binding protein (PBP) NocT unliganded and liganded with the opine nopaline (a condensation product of arginine and α-ketoglurate) and its lactam derivative pyronopaline. NocT exhibited an affinity for pyronopaline (K(D) of 0.6 µM) greater than that for nopaline (KD of 3.7 µM). Although the binding-mode of the arginine part of nopaline/pyronopaline in NocT resembled that of arginine in other PBPs, affinity measurement by two different techniques showed that NocT did not bind arginine. In contrast, NocT presented specific residues such as M117 to stabilize the bound opines. NocT relatives that exhibit the nopaline/pyronopaline-binding mode were only found in genomes of the genus Agrobacterium. Transcriptomics and reverse genetics revealed that A. tumefaciens uses the same pathway for assimilating nopaline and pyronopaline. Fitness measurements showed that NocT is required for a competitive colonization of the plant tumour by A. tumefaciens. Moreover, even though the Ti-plasmid conjugal transfer was not regulated by nopaline, the competitive advantage gained by the nopaline-assimilating Ti-plasmid donors led to a preferential horizontal propagation of this Ti-plasmid amongst the agrobacteria colonizing the plant-tumour niche. This work provided structural and genetic evidences to support the niche construction paradigm in bacterial pathogens.


  • Organizational Affiliation

    Institut des Sciences du Végétal (ISV), UPR2355, CNRS, Saclay Plant sciences, 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): 1 
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OP1
Query on OP1

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
1-[(1S)-4-carbamimidamido-1-carboxybutyl]-5-oxo-D-proline
C11 H18 N4 O5
GTRMYGUJZGMZEF-NKWVEPMBSA-N
PEG
Query on PEG

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

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
G [auth A]
J [auth A]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.57 Å
  • R-Value Free: 0.182 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.168 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.56α = 90
b = 114.56β = 90
c = 37.91γ = 120
Software Package:
Software NamePurpose
DNAdata collection
PHASERphasing
BUSTERrefinement
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-10-29
    Changes: Structure summary
  • Version 1.2: 2016-12-14
    Changes: Structure summary
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description