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)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 58.28 kDa 
• Atom Count: 4066 
• Residue Count: 497 
• Unique protein chains: 2

5MKG

PA3825-EAL Ca-CdG Structure

• DOI: 10.2210/pdb5MKG/pdb
• Entry: 5MKG supersedes: 4Y9O

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


• Deposited: 2016-12-04 Released: 2016-12-14 
• Deposition Author(s): Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.285 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 

Literature

Dimerisation induced formation of the active site and the identification of three metal sites in EAL-phosphodiesterases.

Bellini, D., Horrell, S., Hutchin, A., Phippen, C.W., Strange, R.W., Cai, Y., Wagner, A., Webb, J.S., Tews, I., Walsh, M.A.

(2017) Sci Rep 7: 42166-42166

• PubMed: 28186120 
• DOI: 10.1038/srep42166
• Structures With Same Primary Citation


• PubMed Abstract: 
  

The bacterial second messenger cyclic di-3',5'-guanosine monophosphate (c-di-GMP) is a key regulator of bacterial motility and virulence. As high levels of c-di-GMP are associated with the biofilm lifestyle, c-di-GMP hydrolysing phosphodiesterases (PDEs) have been identified as key targets to aid development of novel strategies to treat chronic infection by exploiting biofilm dispersal. We have studied the EAL signature motif-containing phosphodiesterase domains from the Pseudomonas aeruginosa proteins PA3825 (PA3825 ^EAL ) and PA1727 (MucR ^EAL ). Different dimerisation interfaces allow us to identify interface independent principles of enzyme regulation. Unlike previously characterised two-metal binding EAL-phosphodiesterases, PA3825 ^EAL in complex with pGpG provides a model for a third metal site. The third metal is positioned to stabilise the negative charge of the 5'-phosphate, and thus three metals could be required for catalysis in analogy to other nucleases. This newly uncovered variation in metal coordination may provide a further level of bacterial PDE regulation.

---

Organizational Affiliation: 

Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0FA, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Diguanylate phosphodiesterase	A	256	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: AO964_02925
Protein Feature View is not available: No corresponding UniProt sequence found.

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Diguanylate phosphodiesterase	B	254	Pseudomonas aeruginosa	Mutation(s): 0  Gene Names: AO964_02925
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C2E	A, B	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
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.44 Å
• R-Value Free: 0.285 
• R-Value Work: 0.238 
• R-Value Observed: 0.240 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.23	α = 90
b = 59.4	β = 115.03
c = 92.78	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-12-04 
• Released Date: 2016-12-14 
Deposition Author(s): Horrell, S., Bellini, D., Strange, R., Wagner, A., Walsh, M.
• This entry supersedes: 4Y9O

Revision History 

• Version 1.0: 2016-12-14
  Type: Initial release
  
• Version 1.1: 2017-03-01
  Changes: Database references
• Version 1.2: 2019-05-08
  Changes: Advisory, Data collection, Derived calculations
• Version 1.3: 2019-07-03
  Changes: Data collection, Source and taxonomy