5H5O

A cyclic-GMP-dependent signalling pathway regulates bacterial phytopathogenesis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 
    0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.223 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.230 (Depositor) 

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Ligand Structure Quality Assessment 

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Literature

A cyclic GMP-dependent signalling pathway regulates bacterial phytopathogenesis

An, S.Q.Chin, K.H.Febrer, M.McCarthy, Y.Yang, J.G.Liu, C.L.Swarbreck, D.Rogers, J.Maxwell Dow, J.Chou, S.-H.Ryan, R.P.

(2013) EMBO J 32: 2430-2438

  • DOI: https://doi.org/10.1038/emboj.2013.165
  • Primary Citation of Related Structures:  
    5H5O

  • PubMed Abstract: 

    Cyclic guanosine 3',5'-monophosphate (cyclic GMP) is a second messenger whose role in bacterial signalling is poorly understood. A genetic screen in the plant pathogen Xanthomonas campestris (Xcc) identified that XC_0250, which encodes a protein with a class III nucleotidyl cyclase domain, is required for cyclic GMP synthesis. Purified XC_0250 was active in cyclic GMP synthesis in vitro. The linked gene XC_0249 encodes a protein with a cyclic mononucleotide-binding (cNMP) domain and a GGDEF diguanylate cyclase domain. The activity of XC_0249 in cyclic di-GMP synthesis was enhanced by addition of cyclic GMP. The isolated cNMP domain of XC_0249 bound cyclic GMP and a structure-function analysis, directed by determination of the crystal structure of the holo-complex, demonstrated the site of cyclic GMP binding that modulates cyclic di-GMP synthesis. Mutation of either XC_0250 or XC_0249 led to a reduced virulence to plants and reduced biofilm formation in vitro. These findings describe a regulatory pathway in which cyclic GMP regulates virulence and biofilm formation through interaction with a novel effector that directly links cyclic GMP and cyclic di-GMP signalling.


  • Organizational Affiliation

    Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Diguanylate cyclase
A, B
129Xanthomonas campestris pv. campestris str. B100Mutation(s): 0 
EC: 2.7.7.65
UniProt
Find proteins for B0RM05 (Xanthomonas campestris pv. campestris (strain B100))
Explore B0RM05 
Go to UniProtKB:  B0RM05
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0RM05
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free:  0.259 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.223 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.230 (Depositor) 
Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.648α = 90
b = 48.648β = 90
c = 118.09γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted PCGClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Data collection, Database references, Structure summary