Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 61.97 kDa 
• Atom Count: 4277 
• Modelled Residue Count: 505 
• Deposited Residue Count: 552 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

4AFY

Crystal structure of the FimX EAL domain in complex with reaction product pGpG

• DOI: 10.2210/pdb4AFY/pdb
• NDB: NA2167

• Classification: HYDROLASE
• Organism(s): Pseudomonas aeruginosa PAO1, synthetic construct
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-01-23 Released: 2013-01-09 
• Deposition Author(s): Robert-Paganin, J., Nonin-Lecomte, S., Rety, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

Literature

Crystal Structure of an Eal Domain in Complex with Reaction Product 5'-Pgpg

Robert-Paganin, J., Nonin-Lecomte, S., Rety, S.

(2012) PLoS One 7: 52424

• PubMed: 23285035 
• DOI: 10.1371/journal.pone.0052424
• Primary Citation of Related Structures:  
  4AFY, 4AG0


• PubMed Abstract: 
  

FimX is a large multidomain protein containing an EAL domain and involved in twitching motility in Pseudomonas aeruginosa. We present here two crystallographic structures of the EAL domain of FimX (residues 438-686): one of the apo form and the other of a complex with 5'-pGpG, the reaction product of the hydrolysis of c-di-GMP. In both crystal forms, the EAL domains form a dimer delimiting a large cavity encompassing the catalytic pockets. The ligand is trapped in this cavity by its sugar phosphate moiety. We confirmed by NMR that the guanine bases are not involved in the interaction in solution. We solved here the first structure of an EAL domain bound to the reaction product 5'-pGpG. Though isolated FimX EAL domain has a very low catalytic activity, which would not be significant compared to other catalytic EAL domains, the structure with the product of the reaction can provides some hints in the mechanism of hydrolysis of the c-di-GMP by EAL domains.

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Organizational Affiliation: 

Laboratoire de Cristallographie et RMN biologiques, UMR 8015-Cente National de la Recherche Scientifique, Paris, France.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIMX	A, B	274	Pseudomonas aeruginosa PAO1	Mutation(s): 0  Gene Names: PA4959, fimX EC: 3.1.4.52
UniProt
Find proteins for Q9HUK6 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HUK6  Go to UniProtKB:  Q9HUK6

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*GP*GP)-3'	C, D	2	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	E [auth A], F [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.01 Å
• R-Value Free: 0.239 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.33	α = 90
b = 104.33	β = 90
c = 154.24	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-01-23 
• Released Date: 2013-01-09 
Deposition Author(s): Robert-Paganin, J., Nonin-Lecomte, S., Rety, S.

Revision History  

• Version 1.0: 2013-01-09
  Type: Initial release
  
• Version 1.1: 2013-01-30
  Changes: Database references
• Version 1.2: 2015-10-21
  Changes: Source and taxonomy