Chemistry of Ni2+ in Urease: Sensing, Trafficking, and Catalysis

• Published in: Accounts of chemical research 2011-07, Vol.44 (7), p.520-530
• Main Authors: Zambelli, Barbara, Musiani, Francesco, Benini, Stefano, Ciurli, Stefano
• Format: Article
• Language: English
• Subjects: Availability; Bacillus - enzymology; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Binding Sites; Biocatalysis; Canavalia - enzymology; Carrier Proteins - chemistry; Carrier Proteins - genetics; Carrier Proteins - metabolism; Catalysis; Catalytic Domain; Detection; Enterobacter aerogenes - enzymology; GTP Phosphohydrolases - metabolism; Helicobacter pylori - enzymology; Homeostasis; Ion concentration; Ions - chemistry; Nickel - chemistry; Organisms; Toxicity; Transcription, Genetic; Transition metals; Urease - chemistry; Urease - genetics; Urease - metabolism
• ISSN: 0001-4842; 1520-4898
• DOI: 10.1021/ar200041k

Transition metals are both essential to enzymatic catalysis and limited in environmental availability. These two biological facts have together driven organisms to evolve mechanisms for selective metal ion sensing and utilization. Changes in metal ion concentrations are perceived by metal-dependent transcription factors and transduced into appropriate cellular responses, which regulate the machineries of competitive metal ion homeostasis and metallo-enzyme activation. The intrinsic toxicity of the majority of metal ions further creates a need for regulated intracellular trafficking, which is carried out by specific chaperones. The Ni2+-dependent urease enzymatic system serves as a paradigm for studying the strategies that cells use to handle an essential, yet toxic, metal ion. Although the discovery of urease as the first biological system for which nickel is essential for activity dates to 1975, the rationale for Ni2+ selection, as well as the cascade of events involving metal-dependent gene regulation and protein–protein interactions leading to enzyme activation, have yet to be fully unraveled. The past 14 years since the Account by Hausinger and co-workers (Karplus, P. A.; Pearson, M. A.; Hausinger, R. P. Acc. Chem. Res. 1997, 30, 330–337) have witnessed impressive achievements in the understanding of the biological chemistry of Ni2+ in the urease system. In our Account, we discuss more recent advances in the comprehension of the specific role of Ni2+ in the catalysis and the interplay between Ni2+ and other metal ions, such as Zn2+ and Fe2+, in the metal-dependent enzyme activity. Our discussion focuses on work carried out in our laboratory. In particular, the structural features of the enzyme bound to inhibitors, substrate analogues, and transition state or intermediate analogues have shed light on the catalytic mechanism. Structural and functional information has been correlated to understand the Ni2+ sensing effected by NikR, a nickel-dependent transcription factor. The urease activation process, involving insertion of Ni2+ into the urease active site, has been in part dissected and analyzed through the investigation of the molecular properties of the accessory proteins UreD, UreF, and UreG. The intracellular trafficking of Ni2+ has been rationalized through a deeper understanding of the structural and metal-binding properties of the metallo-chaperone UreE. All the while, a number of key general concepts have been revealed and developed. These inclu