5UYR

Crystal structure of the dark-adapted full-length bacteriophytochrome XccBphP mutant D199A from Xanthomonas campestris


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Pr-favoured variants of the bacteriophytochrome from the plant pathogen Xanthomonas campestris hint on light regulation of virulence-associated mechanisms.

Conforte, V.Otero, L.H.Toum, L.Sirigu, S.Antelo, G.T.Rinaldi, J.Foscaldi, S.Klinke, S.Chavas, L.M.G.Vojnov, A.A.Goldbaum, F.A.Malamud, F.Bonomi, H.R.

(2021) FEBS J 288: 5986-6002

  • DOI: https://doi.org/10.1111/febs.15883
  • Primary Citation of Related Structures:  
    5UYR, 6NDO, 6NDP

  • PubMed Abstract: 

    Red/far-red light-sensing bacteriophytochrome photoreceptor (BphP) pathways play key roles in bacterial physiology and ecology. These bilin-binding proteins photoswitch between two states, Pr (red absorbing) and Pfr (far-red absorbing). The isomerization of the chromophore and the downstream structural changes result in the light signal transduction. The agricultural pathogen Xanthomonas campestris pv. campestris (Xcc) code for a single bathy-like type BphP (XccBphP), previously shown to negatively regulate several light-mediated biological processes involved in virulence. Here, we generated three different full-length variants with single amino acid changes within its GAF domain that affect the XccBphP photocycle favouring its Pr state: L193Q, L193N and D199A. While D199A recombinant protein locks XccBphP in a Pr-like state, L193Q and L193N exhibit a significant enrichment of the Pr form in thermal equilibrium. The X-ray crystal structures of the three variants were solved, resembling the wild-type protein in the Pr state. Finally, we studied the effects of altering the XccBphP photocycle on the exopolysaccharide xanthan production and stomatal aperture assays as readouts of its bacterial signalling pathway. Null-mutant complementation assays show that the photoactive Pr-favoured XccBphP variants L193Q and L193N tend to negatively regulate xanthan production in vivo. In addition, our results indicate that strains expressing these variants also promote stomatal apertures in challenged plant epidermal peels, compared to wild-type Xcc. The findings presented in this work provide new evidence on the Pr state of XccBphP as a negative regulator of the virulence-associated mechanisms by light in Xcc.


  • Organizational Affiliation

    Instituto de Ciencia y Tecnología Dr. César Milstein, Fundación Pablo Cassará, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad de Autónoma de Buenos Aires, Argentina.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bacteriophytochrome
A, B
640Xanthomonas campestris pv. campestris str. 8004Mutation(s): 1 
Gene Names: bphPXC_4241
UniProt
Find proteins for A0A0H2XCS3 (Xanthomonas campestris pv. campestris (strain 8004))
Explore A0A0H2XCS3 
Go to UniProtKB:  A0A0H2XCS3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2XCS3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.45 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.231 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.86α = 90
b = 103.86β = 90
c = 342.61γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-28
    Type: Initial release
  • Version 1.1: 2018-03-21
    Changes: Source and taxonomy
  • Version 1.2: 2021-11-24
    Changes: Database references
  • Version 1.3: 2023-10-04
    Changes: Data collection, Refinement description