PDBsum entry 2zoa

Hydrolase

PDB id: 2zoa

Contents

Protein chains

271 a.a.

Ligands

MLI ×2

Metals

FE2 ×4

Waters ×154

References listed in PDB file

Key reference

• Title: Malonate-Bound structure of the glycerophosphodiesterase from enterobacter aerogenes (gpdq) and characterization of the native fe2+ metal-Ion preference.
• Authors: C.J.Jackson, K.S.Hadler, P.D.Carr, A.J.Oakley, S.Yip, G.Schenk, D.L.Ollis.
• Ref.: Acta Crystallogr Sect F Struct Biol Cryst Commun, 2008, 64, 681-685.
• PubMed id: 18678932

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.