2J4R

Structural Study of the Aquifex aeolicus PPX-GPPA enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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.Biol. 375: 1469

  • DOI: 10.1016/j.jmb.2007.11.073

  • 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 resolu ...

    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.


    Related Citations: 
    • Structural Characterization of the Stringent Response Related Exopolyphosphatase-Guanosine Pentaphosphate Phosphohydrolase Protein Family
      Kristensen, O.,Laurberg, M.,Liljas, A.,Kastrup, J.S.,Gajhede, M.
      (2004) Biochemistry 43: 8894


    Organizational Affiliation

    Biostructural Research, Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark. ok@farma.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EXOPOLYPHOSPHATASE
A, B
308Aquifex aeolicus (strain VF5)Mutation(s): 1 
Gene Names: ppx
Find proteins for O67040 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67040
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4P
Query on G4P

Download SDF File 
Download CCD File 
A
GUANOSINE-5',3'-TETRAPHOSPHATE
C10 H17 N5 O17 P4
BUFLLCUFNHESEH-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.212 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.460α = 90.00
b = 70.460β = 90.00
c = 223.710γ = 120.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-09-05 
  • 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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2018-01-17
    Type: Data collection