Model structures of Helicobacter pylori UreD(H) domains: a putative molecular recognition platform.

The analysis of the sequence of Helicobacter pylori UreD(H), an accessory protein involved in the activation of urease through the assembly of the Ni(2+)-containing active site, revealed the presence of two domains. The structure of these domains was calculated using threading and modeling algorithms. A search for putative binding sites on the protein surface was carried out using dedicated algorithms sensitive to either sequence conservation or structural similarity based on geometry and physicochemical properties. The results suggest that UreD(H) acts as a multifunctional molecular recognition platform facilitating the interaction between apo-urease and the ancillary proteins UreG, UreF, and UreE, responsible for nickel trafficking and delivering.