Mechanism of urea decomposition catalyzed by Sporosarcina pasteurii urease based on quantum chemical calculations

ABSTRACT

To provide theoretical guidance for better healing ability of microbial self-healing concrete, the mechanism of urea decomposition catalyzed by Sporosarcina pasteurii urease in Microbial Induced Carbonate Precipitation was investigated by quantum chemical calculations. The active site model considering bonded residues, non-bonded residues, and flap region residues was established. The formation of initial coordination, the state change of bound water, and the role of residues in the catalytic process were investigated by analysing electrostatic potential, condensed Fukui function, cavity volume, and reaction path using Gaussian, Multiwfn, and POCASA. The results showed that the O atom in urea tended to form initial coordination with Ni1 when urea entered the active site, after which W1 and W3 would be expelled. As the flap region changed from open to closed, W2 would be expelled. Carbamate anion was generated and ammonia was released by the nucleophilic attack of bridging hydroxide (WB) and the proton transfer of Asp363 residue. Carbamic acid was generated and Ni1-WB-Ni2 was regenerated by the proton transfer of Ala366 and Asp363 residues when W4 re-entered the active site. The proton transfer process involving the non-bonded residue Ala366 was the rate-determining step with an energy barrier of 10.39 kcal/mol.

KEYWORDS:

• Microbial self-healing concrete
• Sporosarcina pasteurii urease
• urea
• mechanism
• quantum chemical calculations

Acknowledgments

The financial support of the National Natural Science Foundation of China (grant number 51879092) is gratefully acknowledged. The support of the Fundamental Research Funds for the Central Universities (grant number 2019B52814) is also gratefully acknowledged. This work is also sponsored by Qing Lan Project of Jiangsu Province of China.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The financial support of the National Natural Science Foundation of China (grant number 51879092) is gratefully acknowledged. The support of the Fundamental Research Funds for the Central Universities (grant number 2019B52814) is also gratefully acknowledged. This work is also sponsored by Qing Lan Project of Jiangsu Province of China.