Crystallographic and X-ray absorption spectroscopic characterization of Helicobacter pylori UreE bound to Ni2+ and Zn2+ reveals a role for the disordered C-terminal arm in metal trafficking

Abstract

The survival and growth of the pathogen Helicobacter pylori in the gastric acidic environment is ensured by the activity of urease, an enzyme containing two essential Ni2+ ions in the active site. The metallo-chaperone UreE facilitates in vivo Ni2+ insertion into the apo-enzyme. Crystals of apo-HpUreE and its Ni2+ and Zn2+ bound forms were obtained from protein solutions in the absence and presence of the metal ions. The crystal structures of the homodimeric protein, determined at 2.00 Å (apo), 1.59 Å (Ni) and 2.52 Å (Zn) resolution, show the conserved proximal and solvent-exposed His102 residues from two adjacent monomers invariably involved in metal binding. The C-terminal regions of the apo-protein are disordered in the crystal, but acquire significant ordering in the presence of the metal ions due to the binding of His152. The analysis of X-ray absorption spectral data obtained on solutions of Ni2+- and Zn2+-HpUreE provided accurate information of the metal ion environment in the absence of solid-state effects. These results reveal the role of the histidine residues at the protein C-terminus in metal ion binding, and the mutual influence of protein framework and metal ion stereo-electronic properties in establishing coordination number and geometry leading to metal selectivity.

An XAS investigation of the nickel site structure in the transcriptional regulator InrS

“…Histidine ligands were fit as geometrically rigid imidazole rings with varied angles of rotation (α), with α being defined as the rotation around an axis perpendicular to the plane of the ring and going through the coordinated nitrogen. The distances of the five non-hydrogen atoms in the imidazole ring were thus fit in terms of a single M-N distance for various angles of rotation (α = 0 – 10°)[13–15]. Multiple-scattering parameters for imidazole ligands bound to Ni(II) and Cu(II) were generated using the FEFF6 software package with the imidazole input obtained from average bond lengths and angles gathered from crystallographic data, as previously described[8, 16].…”

Rapid Hydrogen and Oxygen Atom Transfer by a High-Valent Nickel–Oxygen Species

“…Coordination number was explored using single scattering shells with fixed degeneracies which were then varied in integral steps. [57][58][59] To assess the goodness of fit from different models both the R factor (%R) and the reduced χ 2 (χ 2 v ) were minimized. While the R factor is generally expected to decrease with the number of adjustable parameters, χ 2 v may eventually increase, indicating the model is over-fitting the data.…”

Helicobacter pylori hydrogenase accessory protein HypA and urease accessory protein UreG compete with each other for UreE recognition

“…While all four proteins have been well characterized in K. aerogenes , most studies have focused on UreE and UreG in H. pylori. Hp , UreE is a dimeric Ni 2+ and Zn 2+ -binding protein [8–11] thought to be the final Ni 2+ -donor (to urease). Hp , UreG is a GTPase enzyme [12, 13] and GTP hydrolysis is needed for the activation of urease, since site-directed mutagenesis of the conserved P-loop region of UreG abolished urease activity [13].…”