Nickel binding shifts Helicobacter pylori HypA toward compact conformations.

Helicobacter pylori (Hp) is a Gram-negative human pathogen that relies on the nickel enzymes urease and [Ni,Fe]‑hydrogenase for gastric colonization. Delivery of Ni(II) to the active sites of these enzymes is mediated by the metallochaperone HpHypA, which contains a high-affinity structural Zn(II) site and a lower-affinity Ni(II) site, in two distinct domains. Although the NMR solution structure of the apo form Zn-HpHypA is known, the impact of Ni(II) binding on the structure remains unclear. Here, NMR 15N relaxation experiments have been applied to probe the backbone internal dynamics and the rotational diffusion of Zn-HpHypA and Ni,Zn-HpHypA. Residue-resolved model-free analysis revealed broadly similar ps-ns backbone motional amplitudes in the apo and holo states. In contrast, Ni(II) binding increased rotational diffusion, indicating a reduced hydrodynamic radius and a shift toward a more compact conformational ensemble. These observations support a model in which Ni(II) binding generates a delivery-competent protein structure by narrowing the accessible conformational distribution during partner recognition. Previously, calorimetric data reported on the interaction between HpHypA and the urease metallochaperone homodimeric HpUreE2, which showed micromolar Ni(II) binding to HpHypA but the emergence of a sub-nanomolar, strongly exothermic Ni site in the HypA•UreE2 complex. The observed nickel-induced ensemble compaction determined by solution NMR spectroscopy provides a plausible physical basis for Ni-dependent conformational switching to promote high-affinity protein-protein recognition.