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 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.230 

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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 
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
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PCG
Query on PCG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
CYCLIC GUANOSINE MONOPHOSPHATE
C10 H12 N5 O7 P
ZOOGRGPOEVQQDX-UUOKFMHZSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Binding Affinity Annotations 
IDSourceBinding Affinity
PCG Binding MOAD:  5H5O Kd: 293 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.230 
  • 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 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-05-24
    Type: Initial release