Computational modeling of the mechanism of urease

Abstract

In order to elucidate aspects of the mechanism of the hydrolytic enzyme urease, theoretical calculations were undertaken on a model of the active site, using density functional theory. The bridging oxygen donor that has been found in the crystal structures was determined to be a hydroxide ion. The initial coordination of urea at the active site occurs most likely through the urea oxygen to the nickel ion with the lowest coordination number. This coordination can be made without much gain in energy. The calculations also showed that weak coordination of one of the urea amine nitrogen atoms to the second nickel atom is energetically feasible. Furthermore, a proposed mechanism including a tetrahedral intermediate generated by hydrolytic attack on the urea carbon by the bridging hydroxide was modeled, and the tetrahedral intermediate was found to be energetically unfavorable relative to terminal coordination of the substrate (urea).

Figure 1

Schematic depiction of the structure of the active site of Bacillus pasteurii urease [11].

Figure 2

Schematic depiction of two proposed mechanisms for urease, A [11] and B [15].

Figure 3

Structure of complex 2—depicting the initial coordination of urea. The program Molden (see [27]) was used to generate the graphics.

Figure 4

Structure of complex 3. One of the urea nitrogen atoms is coordinated to Ni2, thus replacing the water molecule on Ni2.

Figure 5

A reaction diagram showing the calculated energies of the intermediates found in the computational simulation of the urease reaction with the structures and added small molecules in boxes below (see text for detailed description of the intermediates).

Figure 6

Structure of complex 4—the tetrahedral intermediate. The bridging hydroxide and the urea have moved closer together so that a bond is formed. This was found to release the proton associated with the hydroxide bridge.