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.

Keywords: Catalytic mechanism; Crystal structure; Helicobacter pylori; Klebsiella aerogenes; Nickel; Sporosarcina pasteurii; Urease.

Scheme 1.

Enzymatic steps for the urea hydrolysis

Scheme 2.

Overall reaction of urea hydrolysis

Fig. 1

Ribbon diagram of urease from a K. aerogenes (PDB code: 1EJZ), b S. pasteurii (PDB code: 4CEU), c H. pylori (PDB code: 1E9Z), and d C. ensiformis (jack bean, PDB code: 3LA4). Ribbon colors evidence the chains composing the trimer constituting the minimal quaternary structure of urease. Ni(II) ions are reported as green spheres. The bottom panels of c and d are rotated by 90° around the horizontal axis vs. the top panels

Scheme 3.

Urease mechanism proposed by Blakeley and Zerner (adapted from ref [4])

Fig. 2

Model structures of the active site of K. aerogenes urease (KAU) as evolved from the initial X-ray diffraction data (a PDB code 1KAU; b PDB code 2KAU) to the more recent interpretation (c PDB code 1FWJ). d Displays the ribbon diagram of the active site of KAU, highlighting the mobile flap in the closed conformation depicted according to the B-factor, thus showing the large mobility in this key feature of urease

Scheme 4.

First proposal for the urease reaction mechanism by Hausinger et al. [32]

Scheme 5.

Second proposal for the urease reaction mechanism by Hausinger et al. [29, 50]

Fig. 3

Model structures of the active site of S. pasteurii urease (SPU) as derived from X-ray diffraction data in the native state (a PDB code 2UBP), bound to diamidophosphate, DAP (b PDB code 3UBP) and to boric acid (c PDB code 1S3T)

Scheme 6.

Urease reaction mechanism proposed by Benini et al. [33]

Fig. 4

Ribbon diagram showing the active-site flap of SPU inhibited in the presence of NBPTO and bound to DAP in the open conformation at pH 6.5 (a PDB code 6RP1) and in the closed conformation at pH 7.5 (b PDB code 6RKG). The ribbons are colored according to the crystallographic B-factor. The side chains of αLys220*, αCys322, and αHis323 as well as the two Ni atoms and the bound DAP molecule are also shown

Fig. 5

Model structures of the active site of S. pasteurii urease (SPU) as derived from X-ray diffraction data in the fluoride-inhibited state (a PDB code 4CEX), and in the fluoride-inhibited state bound to urea (b PDB code 6QDY)