2ZO9

Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal ion preference

Summary for 2ZO9

• Entry DOI: 10.2210/pdb2zo9/pdb
• Related: 2DXN 2ZOA
• Descriptor: Phosphohydrolase, FE (II) ION, MALONATE ION, ... (4 entities in total)
• Functional Keywords: malonate, metalloenzyme, iron, phosphodiesterase, hydrolase
• Biological source: Enterobacter aerogenes
• Total number of polymer chains: 2
• Total formula weight: 61972.76

Authors

Jackson, C.J.,Carr, P.D.,Ollis, D.L. (deposition date: 2008-05-07, release date: 2008-10-07, Last modification date: 2024-10-23)

Primary citation

Jackson, C.J.,Hadler, K.S.,Carr, P.D.,Oakley, A.J.,Yip, S.,Schenk, G.,Ollis, D.L.
Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference.
Acta Crystallogr.,Sect.F, 64:681-685, 2008

PubMed Abstract: 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.

PubMed: 18678932
DOI: 10.1107/S1744309108017600

Experimental method

X-RAY DIFFRACTION (2.2 Å)