Open AccessMalonate‐bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe 2+ metal‐ion preference
Author(s) -
Jackson Colin J.,
Hadler Kieran S.,
Carr Paul D.,
Oakley Aaron J.,
Yip Sylvia,
Schenk Gerhard,
Ollis David L.
Publication year - 2008
Publication title -
acta crystallographica section f
Language(s) - English
Resource type - Journals
ISSN - 1744-3091
DOI - 10.1107/s1744309108017600
Subject(s) - enterobacter aerogenes , malonate , metal , chemistry , diethyl malonate , crystallography , active site , ion , resolution (logic) , stereochemistry , inorganic chemistry , enzyme , catalysis , organic chemistry , biochemistry , escherichia coli , gene , artificial intelligence , computer science
The structure of a malonate‐bound form of the glycerophosphodiesterase from Enterobacter aerogenes , GpdQ, has been refined at a resolution of 2.2 Å to a final R factor of 17.1%. The structure was originally solved to 2.9 Å resolution using SAD phases from Zn 2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367 , 1047–1062]. However, the 2.9 Å resolution was insufficient to discern significant details of the architecture of the binuclear metal centre that constitutes the active site. Furthermore, kinetic analysis revealed that the enzyme lost a significant amount of activity in the presence of Zn 2+ , suggesting that it is unlikely to be a catalytically relevant metal ion. In this communication, a higher resolution structure of GpdQ is presented in which malonate is visibly coordinated in the active site and analysis of the native metal‐ion preference is presented using atomic absorption spectroscopy and anomalous scattering. Catalytic implications of the structure and its Fe 2+ metal‐ion preference are discussed.