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

Journal Article


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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.

Authors


  •   Jackson, Colin J. (external author)
  •   Hadler, Kieran S. (external author)
  •   Carr, Paul D. (external author)
  •   Oakley, Aaron J.
  •   Yip, Sylvia (external author)
  •   Schenk, Gerhard (external author)
  •   Ollis, David L. (external author)

Publication Date


  • 2008

Citation


  • Jackson, C. J., Hadler, K. S., Carr, P. D., Oakley, A. J., Yip, S., Schenk, G. & Ollis, D. L. (2008). Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallographica Section F: Structural Biology and Crystallization Communications Online, 64 (8), 681-685.

Scopus Eid


  • 2-s2.0-49249116616

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1932&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/893

Number Of Pages


  • 4

Start Page


  • 681

End Page


  • 685

Volume


  • 64

Issue


  • 8

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.

Authors


  •   Jackson, Colin J. (external author)
  •   Hadler, Kieran S. (external author)
  •   Carr, Paul D. (external author)
  •   Oakley, Aaron J.
  •   Yip, Sylvia (external author)
  •   Schenk, Gerhard (external author)
  •   Ollis, David L. (external author)

Publication Date


  • 2008

Citation


  • Jackson, C. J., Hadler, K. S., Carr, P. D., Oakley, A. J., Yip, S., Schenk, G. & Ollis, D. L. (2008). Malonate-bound structure of the glycerophosphodiesterase from Enterobacter aerogenes (GpdQ) and characterization of the native Fe2+ metal-ion preference. Acta Crystallographica Section F: Structural Biology and Crystallization Communications Online, 64 (8), 681-685.

Scopus Eid


  • 2-s2.0-49249116616

Ro Full-text Url


  • http://ro.uow.edu.au/cgi/viewcontent.cgi?article=1932&context=scipapers

Ro Metadata Url


  • http://ro.uow.edu.au/scipapers/893

Number Of Pages


  • 4

Start Page


  • 681

End Page


  • 685

Volume


  • 64

Issue


  • 8