2J4R | pdb_00002j4r

Structural Study of the Aquifex aeolicus PPX-GPPA enzyme

• PDB DOI: https://doi.org/10.2210/pdb2J4R/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2006-09-05 Released: 2007-10-16 
• Deposition Author(s): Kristensen, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free: 
  0.296 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.212 (Depositor) 

Starting Model: experimental

Literature

Structure of the Ppx/Gppa Phosphatase from Aquifex Aeolicus in Complex with the Alarmone Ppgpp

Kristensen, O., Ross, B., Gajhede, M.

(2008) J Mol Biology 375: 1469

• PubMed: 18155044 
• DOI: https://doi.org/10.1016/j.jmb.2007.11.073
• Primary Citation Related Structures: 
  2J4R


• PubMed Abstract: 
  

  The crystal structure of the prototype exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family member from Aquifex aeolicus in complex with the intracellular second messenger guanosine tetraphosphate was determined at 2.7-A resolution. The hydrolytic base is identified as E119. The dual specificity established for the Escherichia coli homolog is shown to be compatible with a common active site for guanosine pentaphosphate and polyphosphate hydrolysis. Distinct and different degrees of closure between the two domains of the enzyme are associated with substrate binding. The arginines R22 and R267, residing in different domains, are crucial for guanosine pentaphosphate specificity as they interact with the unique 3'-ribose phosphorylation.

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Organizational Affiliation: 
• Biostructural Research, Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark. [e-mail]

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content 

• Total Structure Weight: 70.6 kDa 
• Atom Count: 4,997 
• Modeled Residue Count: 600 
• Deposited Residue Count: 616 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EXOPOLYPHOSPHATASE	A, B	308	Aquifex aeolicus	Mutation(s): 1
UniProt
Find proteins for O67040 (Aquifex aeolicus (strain VF5)) Explore O67040  Go to UniProtKB:  O67040

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
G4P	C [auth A]	GUANOSINE-5',3'-TETRAPHOSPHATE C10 H17 N5 O17 P4 BUFLLCUFNHESEH-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.71 Å
• R-Value Free:  0.296 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.212 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.46	α = 90
b = 70.46	β = 90
c = 223.71	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-10-16 
Deposition Author(s): Kristensen, O.

Revision History  

• Version 1.0: 2007-10-16
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection
• Version 1.4: 2023-12-13
  Changes: Data collection, Database references, Other, Refinement description, Structure summary