Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

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Structures of the PelD Cyclic Diguanylate Effector Involved in Pellicle Formation in Pseudomonas aeruginosa PAO1.

Li, Z.Chen, J.H.Hao, Y.Nair, S.K.

(2012) J Biol Chem 287: 30191-30204

  • DOI: https://doi.org/10.1074/jbc.M112.378273
  • Primary Citation of Related Structures:  
    4ETX, 4ETZ, 4EU0, 4EUV

  • PubMed Abstract: 

    The second messenger bis-(3'-5')-cyclic dimeric guanosine monophosphate (c-di-GMP) plays a vital role in the global regulation in bacteria. Here, we describe structural and biochemical characterization of a novel c-di-GMP effector PelD that is critical to the formation of pellicles by Pseudomonas aeruginosa. We present high-resolution structures of a cytosolic fragment of PelD in apo form and its complex with c-di-GMP. The structure contains a bi-domain architecture composed of a GAF domain (commonly found in cyclic nucleotide receptors) and a GGDEF domain (found in c-di-GMP synthesizing enzymes), with the latter binding to one molecule of c-di-GMP. The GGDEF domain has a degenerate active site but a conserved allosteric site (I-site), which we show binds c-di-GMP with a K(d) of 0.5 μm. We identified a series of residues that are crucial for c-di-GMP binding, and confirmed the roles of these residues through biochemical characterization of site-specific variants. The structures of PelD represent a novel class of c-di-GMP effector and expand the knowledge of scaffolds that mediate c-di-GMP recognition.

  • Organizational Affiliation

    Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PelD298Pseudomonas aeruginosa PAO1Mutation(s): 0 
Gene Names: PA3061pelD
Find proteins for Q9HZE7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Explore Q9HZE7 
Go to UniProtKB:  Q9HZE7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HZE7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C2E

Download Ideal Coordinates CCD File 
B [auth A]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
Binding Affinity Annotations 
IDSourceBinding Affinity
C2E Binding MOAD:  4EU0 Kd: 400 (nM) from 1 assay(s)
PDBBind:  4EU0 Kd: 400 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.517α = 90
b = 41.395β = 109.92
c = 62.912γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-25
    Type: Initial release
  • Version 1.1: 2012-09-19
    Changes: Database references
  • Version 1.2: 2024-02-28
    Changes: Data collection, Database references, Derived calculations, Structure summary