The structure-based reaction mechanism of urease, a nickel dependent enzyme: tale of a long debate

Abstract

This review is an attempt to retrace the chronicle that starts from the discovery of the role of nickel as the essential metal ion in urease for the enzymatic catalysis of urea, a key step in the biogeochemical cycle of nitrogen on Earth, to the most recent progress in understanding the chemistry of this historical enzyme. Data and facts are presented through the magnifying lenses of the authors, using their best judgment to filter and elaborate on the many facets of the research carried out on this metalloenzyme over the years. The tale is divided in chapters that discuss and describe the results obtained in the subsequent leaps in the knowledge that led from the discovery of a biological role for Ni to the most recent advancements in the comprehension of the relationship between the structure and function of urease. This review is intended not only to focus on the bioinorganic chemistry of this beautiful metal-based catalysis, but also, and maybe primarily, to evoke inspiration and motivation to further explore the realm of bio-based coordination chemistry.

Cryo-EM structure of Helicobacter pylori urease with an inhibitor in the active site at 2.0 Å resolution

“…Ureases form stable C 3 trimers, although some occur in higher-order arrangements, either as D 3 dimers of trimers or as tetrahedral (T) tetramers of trimers. In the native state of the enzyme, a hydroxide anion has been reported to bridge the two nickel ions, primed for nucleophilic attack on the substrate during hydrolysis [18][19][20] .…”

Effect of Heavy Metal Contamination on Soil Enzymes Activities

“…Urease activity in soil has the capacity of the enzyme to catalyze the transformation of urea into ammonium (Kandeler et al, 1999). And play a critical role in the global nitrogen cycle's mineralization step, catalyzing the rapid hydrolytic decomposition of urea to produce ammonia and carbamate, the latter of which decomposes spontaneously into a second molecule of ammonia and bicarbonate (Blakeley et al, 1969;Mazzei et al, 2020).…”

“…From Figure 3, ammonia formed by the decomposition of urea into a second molecule of ammonia and bicarbonate in 24 hours was used to determine Urease activity (Blakeley et al, 1969;Mazzei et al, 2020), making Cadmium reaction effective on its activity. Higher levels of ammonia indicated higher urease activity, but an increase in Cd concentration affects Urease's respiration process, resulting in a gradual decrease in urease activity in the soil (Doelman & Haanstra, 1986;Zheng et al, 2019).…”

Enhancement of Thermostability of Aspergillus flavus Urate Oxidase by Immobilization on the Ni-Based Magnetic Metal–Organic Framework

“…Among them, nickel-based MOFs have gained more interest not only because they have been demonstrated to have great application prospects for supercapacitors, but also because they could be the template/precursor for unique metal oxide and carbon materials with a specific structure, especially the Ni 3 (BTC) 2 ·12H 2 O (BTC = 1,3,5-benzene tricarboxylic acid) [ 38 , 39 , 40 , 41 , 42 ]. Besides, many authors have mentioned the good interaction between Ni and His-tagged enzymes where synthesized NPs have a porous structure and there are Ni atoms in the surface and inside the pores; good coordination between Ni atoms and enzymes has been reported [ 43 ]. On the other hand, magnetic nanoparticles (NPs) are attractive materials for enzyme immobilization and other applications, and, in view of their superparamagnetism, they can be accessed by remote stimuli [ 44 , 45 , 46 , 47 ].…”