Enzymatic Catalysis of Urea Decomposition:  Elimination or Hydrolysis?

Abstract

We present a high-level quantum chemical study of possible reaction mechanisms associated with the catalytic decomposition of urea by a bioinorganic mimetic of the dinickel active site of urease. We chose the phthalazine-dinickel complexes of Lippard and co-workers, because these mimetics have been shown to hydrolytically degrade urea. High-level quantum chemical methodologies were utilized to identify stable intermediates and transition-state structures along several possible reaction pathways. The computed results were then used to further analyze what may occur in the active site of urease. Valuable information on the latter has been extracted from experimental data, computational approaches, and unpublished molecular dynamics simulations. On the basis of these comparative studies, we propose that both the elimination and hydrolytic pathways may compete for urea decomposition in the active site of urease.

Synthetic Models for the Active Sites of Nickel‐Containing Enzymes

“…It remains unclear, however, which binding mode of urea (terminal or bridging as found in 90) facilitates the elimination reaction. Ammonia elimination from the O-bound terminal substrate appears to be in accordance with quantum chemical studies on that model system [187]. When the reaction was carried out in 50% aqueous acetonitrile solution, ammonia was produced at the same rate but without buildup of the cyanate-containing product, suggesting that the latter is hydrolyzed in the presence of water.…”

“…This has been taken as indication that a cyanate intermediate may also be relevant for the enzyme, and a high-level computational study by Estiu and Merz on urea decomposition promoted by Lippard's phtalazine-based dinickel model complexes led the authors to propose that both the elimination and hydrolytic pathways may indeed compete in the urease active site [187]. The fi rst experimental evidence for the transformation of urea to cyanate at dinickel(II) sites came from the groups of Okawa [162] and Meyer [167] [167].…”

Why Urea Eliminates Ammonia Rather than Hydrolyzes in Aqueous Solution

“…[1][2][3][4] In contrast, when catalyzed by ureases, urea is generally believed to undergo hydrolysis rather than ammonia elimination. [4][5][6][7][8][9][10][11][12][13][14][15][16][17][18] The products of hydrolytic decomposition have been reported to be either HCO 3 − and NH 4 + or ammonium carbamate depending on the buffer system. 19 These products are most readily rationalized to arise from an addition-elimination sequence.…”

A Biomimetic Nano-Scale Aggregation Route for the Formation of Submicron-Size Colloidal Calcite Particles

“…1989; Estiu & Merz, 2004). It also appears that urease participates in systemic nitrogentransport pathways and possibly acts as a toxic defense protein (Mobley & Hausinger, 1989).…”