Structural characterization of Zn(II)-, Co(II)-, and Mn(II)-loaded forms of the argE-encoded N-acetyl-L-ornithine deacetylase from Escherichia coli

The Zn, Co, and Mn K-edge extended X-ray absorption fine structure (EXAFS) spectra of the N-acetyl-l-ornithine deacetylase (ArgE) from Escherichia coli, loaded with one or two equivalents of divalent metal ions (i.e., [Zn(II)_(ArgE)], [Zn(II)Zn(II)(ArgE)], [Co(II)_(ArgE)], [Co(II)Co(II)(ArgE)], [Mn(II)_(ArgE)], and [Mn(II)Mn(II)(ArgE)]), were recorded. The Fourier transformed data (FT) for [Zn(II)_(ArgE)], [Zn(II)Zn(II)(ArgE)], [Co(II)_(ArgE)] and [Co(II)Co(II)(ArgE)] are dominated by a peak at 2.05 Å, that can be fit assuming five or six light atom (N,O) scatterers. Inclusion of multiple-scattering contributions from the outer-shell atoms of a histidine-imidazole ring resulted in reasonable Debye–Waller factors for these contributions and a slight reduction in the goodness-of-fit value (f′). Furthermore, the data best fit a model that included a M–M vector at 3.3 and 3.4 Å for Zn(II) and Co(II), respectively, suggesting the formation of a dinuclear site. Multiple scattering contributions from the outer-shell atoms of a histidine-imidazole rings are observed at ~ 3 and 4 Å for Zn(II)- and Co(II)-loaded ArgE suggesting at least one histidine ligand at each metal binding site. Likewise, EXAFS data for Mn(II)-loaded ArgE are dominated by a peak at 2.19 Å that was best fit assuming six light atom (N,O) scatterers. Due to poor signal to noise ratios for the Mn EXAFS spectra, no Mn–Mn vector could be modeled. Peak intensities for [M(II)_(ArgE)] vs. [M(II)M(II)(ArgE)] suggest the Zn(II), Co(II), and Mn(II) bind to ArgE in a cooperative manner. Since no structural data has been reported for any ArgE enzyme, the EXAFS data reported herein represent the first structural glimpse for ArgE enzymes. These data also provide a structural foundation for the future design of small molecules that function as inhibitors of ArgE and may potentially function as a new class of antibiotics.

The Zn, Co, and Mn K-edge EXAFS spectra of N-acetyl-L-ornithine deacetylase (ArgE) from E. coli are presented. The Fourier transformed data for Zn(II) and Co(II)-loaded ArgE indicate five or six N,O scatterers at 2.05 Å and a M-M vector at ~ 3.4 Å suggesting the formation of a dinuclear site.Figure optionsDownload as PowerPoint slideHighlights
► The Zn, Co, and Mn K-edge EXAFS spectra of ArgE.
► EXAFS data for Zn(II) and Co(II) ArgE exhibit a peak at 2.05 Å, indicating five or six N,O scatterers.
► Inclusion of a M-M vector 3.4 Å for Zn(II) or Co(II) ArgE suggests the formation of a dinuclear site.
► These data provide a structural base for the future design of small molecule inhibitors of ArgE.