4DN0 | pdb_00004dn0

PelD 156-455 from Pseudomonas aeruginosa PA14 in complex with c-di-GMP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.252 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.206 (Depositor) 

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Ligand Structure Quality Assessment 

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This is version 1.3 of the entry. See complete history


Literature

Structure of the Cytoplasmic Region of PelD, a Degenerate Diguanylate Cyclase Receptor That Regulates Exopolysaccharide Production in Pseudomonas aeruginosa.

Whitney, J.C.Colvin, K.M.Marmont, L.S.Robinson, H.Parsek, M.R.Howell, P.L.

(2012) J Biological Chem 287: 23582-23593

  • DOI: https://doi.org/10.1074/jbc.M112.375378
  • Primary Citation of Related Structures:  
    4DMZ, 4DN0

  • PubMed Abstract: 

    High cellular concentrations of bis-(3',5')-cyclic dimeric guanosine mono-phosphate (c-di-GMP) regulate a diverse range of phenotypes in bacteria including biofilm development. The opportunistic pathogen Pseudomonas aeruginosa produces the PEL polysaccharide to form a biofilm at the air-liquid interface of standing cultures. Among the proteins required for PEL polysaccharide production, PelD has been identified as a membrane-bound c-di-GMP-specific receptor. In this work, we present the x-ray crystal structure of a soluble cytoplasmic region of PelD in its apo and c-di-GMP complexed forms. The structure of PelD reveals an N-terminal GAF domain and a C-terminal degenerate GGDEF domain, the latter of which binds dimeric c-di-GMP at an RXXD motif that normally serves as an allosteric inhibition site for active diguanylate cyclases. Using isothermal titration calorimetry, we demonstrate that PelD binds c-di-GMP with low micromolar affinity and that mutation of residues involved in binding not only decreases the affinity of this interaction but also abrogates PEL-specific phenotypes in vivo. Bioinformatics analysis of the juxtamembrane region of PelD suggests that it contains an α-helical stalk region that connects the soluble region to the transmembrane domains and that similarly to other GAF domain containing proteins, this region likely forms a coiled-coil motif that mediates dimerization. PelD with Alg44 and BcsA of the alginate and cellulose secretion systems, respectively, collectively constitute a group of c-di-GMP receptors that appear to regulate exopolysaccharide assembly at the protein level through activation of their associated glycosyl transferases.


  • Organizational Affiliation

    Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 1X8, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putative uncharacterized protein pelD321Pseudomonas aeruginosa UCBPP-PA14Mutation(s): 0 
Gene Names: pelDPA14_24510
UniProt
Find proteins for A0A0H2ZD98 (Pseudomonas aeruginosa (strain UCBPP-PA14))
Explore A0A0H2ZD98 
Go to UniProtKB:  A0A0H2ZD98
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0H2ZD98
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.252 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.206 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 41.776α = 90
b = 82.043β = 90
c = 91.808γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted C2EClick on this verticalbar to view details

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-23
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Database references
  • Version 1.2: 2012-07-25
    Changes: Database references
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary