2DXN

Glycerophosphodiesterase from Enterobacter aerogenes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The structure and function of a novel glycerophosphodiesterase from Enterobacter aerogenes

Jackson, C.J.Carr, P.D.Liu, J.W.Watt, S.J.Beck, J.L.Ollis, D.L.

(2007) J.Mol.Biol. 367: 1047-1062

  • DOI: 10.1016/j.jmb.2007.01.032
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The structure of the glycerophosphodiesterase (GDPD) from Enterobacter aerogenes, GpdQ, has been solved by SAD phasing from the active site metal ions. Structural analysis indicates that GpdQ belongs to the alpha/beta sandwich metallo-phosphoesterase ...

    The structure of the glycerophosphodiesterase (GDPD) from Enterobacter aerogenes, GpdQ, has been solved by SAD phasing from the active site metal ions. Structural analysis indicates that GpdQ belongs to the alpha/beta sandwich metallo-phosphoesterase family, rather than the (alpha/beta)(8) barrel GDPD family, suggesting that GpdQ is a structurally novel GDPD. Hexameric GpdQ is generated by interactions between three dimers. The dimers are formed through domain swapping, stabilised by an inter-chain disulfide bond, and beta-sheet extension. The active site contains a binuclear metal centre, with a fully occupied alpha-metal ion site, and partially occupied beta-metal ion site, as revealed by anomalous scattering analysis. Using a combination of TLS refinement and normal mode analysis, the dynamic movement of GpdQ was investigated. This analysis suggests that the hexameric quaternary structure stabilises the base of the dimer, which promotes "breathing" of the active site cleft. Comparison with other metallo-phosphodiesterases shows that although the central, catalytic, domain is highly conserved, many of these enzymes possess structurally unrelated secondary domains located at the entrance of the active site. We suggest that this could be a common structural feature of metallo-phosphodiesterases that constrains substrate specificity, preventing non-specific phosphodiester hydrolysis.


    Related Citations: 
    • The purification, crystallization and preliminary diffraction of a glycerophosphodiesterase from Enterobacter aerogenes
      Jackson, C.J.,Carr, P.D.,Kim, H.K.,Liu, J.W.,Ollis, D.L.
      (2006) Acta Crystallogr.,Sect.F 62: 659


    Organizational Affiliation

    Research School of Chemistry, Australian National University, ACT, 0200, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Phosphohydrolase
A, B
274Klebsiella aerogenesMutation(s): 0 
Gene Names: cpdA (ph)
EC: 3.1.4.53
Find proteins for Q6XBH1 (Klebsiella aerogenes)
Go to UniProtKB:  Q6XBH1
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • Space Group: P 21 3
Unit Cell:
Length (Å)Angle (°)
a = 164.274α = 90.00
b = 164.274β = 90.00
c = 164.274γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
HKL-2000data collection
MLPHAREphasing
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Advisory, Derived calculations, Version format compliance