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 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.3 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:  
    2DXL, 2DXN

  • 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 family, rather than the (alpha/beta)(8) barrel GDPD family, suggesting that GpdQ is a structurally novel GDPD ...

    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 Struct Biol Cryst Commun 62: 659

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PhosphohydrolaseA, B274Klebsiella aerogenesMutation(s): 0 
Gene Names: GpdQcpdAph
EC: 3.1.4.46 (PDB Primary Data), 3.1.4.53 (UniProt)
UniProt
Find proteins for Q6XBH1 (Klebsiella aerogenes)
Explore Q6XBH1 
Go to UniProtKB:  Q6XBH1
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.92 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.162 
  • R-Value Observed: 0.164 
  • Space Group: P 21 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.274α = 90
b = 164.274β = 90
c = 164.274γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Derived calculations, Version format compliance
  • Version 1.3: 2019-12-11
    Changes: Data collection