Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 34.02 kDa 
• Atom Count: 2430 
• Residue Count: 286 
• Unique protein chains: 1

4EUV

Crystal Structure of PelD 158-CT from Pseudomonas aeruginosa PAO1, in complex with c-di-GMP, form 1

• DOI: 10.2210/pdb4EUV/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Pseudomonas aeruginosa PAO1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-04-25 Released: 2012-07-25 
• Deposition Author(s): Li, Z., Chen, J., Nair, S.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.281 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 

Literature

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

• PubMed: 22810222 
• DOI: 10.1074/jbc.M112.378273
• Structures With Same Primary Citation


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
PelD	A	297	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA3061, pelD
Find proteins for Q9HZE7 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Go to UniProtKB:  Q9HZE7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	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 PKFDLKSEZWEFGL-MHARETSRSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C2E	Kd:  500   nM  Binding MOAD
C2E	Kd :  500   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.281 
• R-Value Work: 0.221 
• R-Value Observed: 0.224 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.531	α = 90
b = 41.516	β = 110.95
c = 64.402	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-04-25 
• Released Date: 2012-07-25 
Deposition Author(s): Li, Z., Chen, J., Nair, S.K.

Revision History 

• Version 1.0: 2012-07-25
  Type: Initial release
  
• Version 1.1: 2012-09-19
  Changes: Database references