5EUH

Crystal structure of the c-di-GMP-bound GGDEF domain of P. fluorescens GcbC

  • Classification: MEMBRANE PROTEIN
  • Organism(s): Pseudomonas fluorescens Pf0-1
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2015-11-18 Released: 2015-12-30 
  • Deposition Author(s): Giglio, K.M., Cooley, R.B., Sondermann, H.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Contribution of Physical Interactions to Signaling Specificity between a Diguanylate Cyclase and Its Effector.

Dahlstrom, K.M.Giglio, K.M.Collins, A.J.Sondermann, H.O'Toole, G.A.

(2015) mBio 6: e01978-e01915

  • DOI: 10.1128/mBio.01978-15
  • Primary Citation of Related Structures:  
    5EUH

  • PubMed Abstract: 
  • Cyclic diguanylate (c-di-GMP) is a bacterial second messenger that controls multiple cellular processes. c-di-GMP networks have up to dozens of diguanylate cyclases (DGCs) that synthesize c-di-GMP along with many c-di-GMP-responsive target proteins t ...

    Cyclic diguanylate (c-di-GMP) is a bacterial second messenger that controls multiple cellular processes. c-di-GMP networks have up to dozens of diguanylate cyclases (DGCs) that synthesize c-di-GMP along with many c-di-GMP-responsive target proteins that can bind and respond to this signal. For such networks to have order, a mechanism(s) likely exists that allow DGCs to specifically signal their targets, and it has been suggested that physical interactions might provide such specificity. Our results show a DGC from Pseudomonas fluorescens physically interacting with its target protein at a conserved interface, and this interface can be predictive of DGC-target protein interactions. Furthermore, we demonstrate that physical interaction is necessary for the DGC to maximally signal its target. If such "local signaling" is a theme for even a fraction of the DGCs used by bacteria, it becomes possible to posit a model whereby physical interaction allows a DGC to directly signal its target protein, which in turn may help curtail undesired cross talk with other members of the network.


    Organizational Affiliation

    Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire georgeo@dartmouth.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Putative GGDEF domain membrane proteinABCD172Pseudomonas fluorescens Pf0-1Mutation(s): 0 
Gene Names: Pfl01_4666
Find proteins for Q3K751 (Pseudomonas fluorescens (strain Pf0-1))
Explore Q3K751 
Go to UniProtKB:  Q3K751
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C2E
Query on C2E

Download Ideal Coordinates CCD File 
A, B, C
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.99 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.227 
  • Space Group: P 62
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.913α = 90
b = 141.913β = 90
c = 106.169γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01-AI097307
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM-103485
National Science Foundation (NSF, United States)United StatesDMR-1332208

Revision History 

  • Version 1.0: 2015-12-30
    Type: Initial release
  • Version 1.1: 2016-02-10
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Derived calculations
  • Version 1.3: 2019-11-27
    Changes: Author supporting evidence