Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.
The structure of a malonate-bound form of the glycerophosphodiesterase from Enterobacter aerogenes, GpdQ, has been refined at a resolution of 2.2 A to a final R factor of 17.1%. The structure was originally solved to 2.9 A resolution using SAD phases from Zn2+ metal ions introduced into the active site of the apoenzyme [Jackson et al. (2007), J. Mol. Biol. 367, 1047-1062]. However, the 2.9 A 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 Zn2+, 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 Fe2+ metal-ion preference are discussed.
Jackson
Colin J
CJ
Research School of Chemistry, Australian National University, Australia.
Hadler
Kieran S
KS
Carr
Paul D
PD
Oakley
Aaron J
AJ
Yip
Sylvia
S
Schenk
Gerhard
G
Ollis
David L
DL
D018360:Crystallography, X-Ray; D021902:Enterobacter aerogenes / Q000201:enzymology*; D007501:Iron / Q000378:metabolism*; D008314:Malonates / Q000378:metabolism*; D008958:Models, Molecular; D010727:Phosphoric Diester Hydrolases / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D013054:Spectrophotometry, Atomic
D008314:Malonates; C030290:malonic acid; D007501:Iron; D010727:Phosphoric Diester Hydrolases; C038133:glycerophosphodiester phosphodiesterase