1T6C

Structural characterization of the Ppx/GppA protein family: crystal structure of the Aquifex aeolicus family member


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 8894-8900

  • DOI: 10.1021/bi049083c
  • Primary Citation of Related Structures:  
  • Also Cited By: 2J4R

  • PubMed Abstract: 
  • Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes play central roles in the bacterial stringent response induced by starvation. The high-resolution crystal structure of the putative Aquifex aeolicus PPX/GPPA phosphatase ...

    Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes play central roles in the bacterial stringent response induced by starvation. The high-resolution crystal structure of the putative Aquifex aeolicus PPX/GPPA phosphatase from the actin-like ATPase domain superfamily has been determined, providing the first insights to features of the common catalytic core of the PPX/GPPA family. The protein has a two-domain structure with an active site located in the interdomain cleft. Two crystal forms were investigated (type I and II) at resolutions of 1.53 and 2.15 A, respectively. This revealed a structural flexibility that has previously been described as a "butterfly-like" cleft opening around the active site in other actin-like superfamily proteins. A calcium ion is observed at the center of this region in type I crystals, substantiating that PPX/GPPA enzymes use metal ions for catalysis. Structural analysis suggests that nucleotides bind at a similar position to that seen in other members of the superfamily.


    Related Citations: 
    • Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily
      Reizer, J.,Reizer, A.,Saier Jr., M.H.,Bork, P.,Sander, C.
      (1993) Trends Biochem.Sci. 18: 247
    • Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli
      Kuroda, A.,Nomura, K.,Ohtomo, R.,Kato, J.,Ikeda, T.,Takiguchi, N.,Ohtake, H.,Kornberg, A.
      (2001) Science 293: 705
    • Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase
      Keasling, J.D.,Bertsch, L.,Kornberg, A.
      (1993) Proc.Natl.Acad.Sci.USA 90: 7029


    Organizational Affiliation

    Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark. ok@dfuni.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
exopolyphosphatase
A
315Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: ppx
Find proteins for O67040 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O67040
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IOD
Query on IOD

Download SDF File 
Download CCD File 
A
IODIDE ION
I
XMBWDFGMSWQBCA-UHFFFAOYSA-M
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
A
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.217 
  • R-Value Work: 0.162 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.776α = 90.00
b = 70.287β = 90.00
c = 90.783γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
ARP/wARPmodel building
CNSphasing
CCP4data scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-08-03
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Source and taxonomy, Version format compliance