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

催化作用 尿素酶 活动站点 化学 尿素 残留物(化学) 氢氧化物 无机化学 有机化学
作者
Jingdong Zhu,Dejian Shen,Jingjing Xie,Chunmei Tang,Baosheng Jin,Shengxing Wu
出处
期刊:Molecular Simulation [Taylor & Francis]
卷期号:47 (16): 1335-1348 被引量:7
标识
DOI:10.1080/08927022.2021.1970156
摘要

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.
最长约 10秒,即可获得该文献文件

科研通智能强力驱动
Strongly Powered by AbleSci AI
更新
PDF的下载单位、IP信息已删除 (2025-6-4)

科研通是完全免费的文献互助平台,具备全网最快的应助速度,最高的求助完成率。 对每一个文献求助,科研通都将尽心尽力,给求助人一个满意的交代。
实时播报
NexusExplorer应助灵巧鑫采纳,获得30
刚刚
刚刚
共享精神应助鲤跃采纳,获得10
1秒前
SYLH应助橙子采纳,获得20
1秒前
特安谭完成签到,获得积分10
1秒前
2秒前
RoKing完成签到,获得积分10
2秒前
ding完成签到,获得积分10
3秒前
胡志飞发布了新的文献求助10
3秒前
科研通AI2S应助嗷嗷采纳,获得10
3秒前
zzz发布了新的文献求助10
4秒前
深情安青应助好宝宝采纳,获得10
4秒前
4秒前
4秒前
4秒前
5秒前
Noah完成签到 ,获得积分10
5秒前
SciGPT应助大冰采纳,获得10
5秒前
量子星尘发布了新的文献求助80
5秒前
天边发布了新的文献求助10
6秒前
未央歌完成签到 ,获得积分10
6秒前
6秒前
Xinger完成签到,获得积分10
7秒前
8秒前
sssaw发布了新的文献求助10
8秒前
RoKing发布了新的文献求助10
9秒前
香蕉觅云应助zy采纳,获得10
9秒前
Xinger发布了新的文献求助10
10秒前
xiaozhiok发布了新的文献求助10
10秒前
思垢发布了新的文献求助10
10秒前
11秒前
zjh完成签到,获得积分10
12秒前
13秒前
好想走到伯纳乌完成签到,获得积分10
13秒前
Rondab应助mariawang采纳,获得10
13秒前
田様应助ly楠采纳,获得10
13秒前
李爱国应助天边采纳,获得10
14秒前
大模型应助RoKing采纳,获得10
15秒前
kd发布了新的文献求助10
15秒前
胡志飞完成签到,获得积分20
15秒前
高分求助中
A new approach to the extrapolation of accelerated life test data 1000
ACSM’s Guidelines for Exercise Testing and Prescription, 12th edition 500
‘Unruly’ Children: Historical Fieldnotes and Learning Morality in a Taiwan Village (New Departures in Anthropology) 400
Indomethacinのヒトにおける経皮吸収 400
Phylogenetic study of the order Polydesmida (Myriapoda: Diplopoda) 370
基于可调谐半导体激光吸收光谱技术泄漏气体检测系统的研究 350
Robot-supported joining of reinforcement textiles with one-sided sewing heads 320
热门求助领域 (近24小时)
化学 材料科学 医学 生物 工程类 有机化学 生物化学 物理 内科学 纳米技术 计算机科学 化学工程 复合材料 遗传学 基因 物理化学 催化作用 冶金 细胞生物学 免疫学
热门帖子
关注 科研通微信公众号,转发送积分 3988732
求助须知:如何正确求助?哪些是违规求助? 3531027
关于积分的说明 11252281
捐赠科研通 3269732
什么是DOI,文献DOI怎么找? 1804764
邀请新用户注册赠送积分活动 881869
科研通“疑难数据库(出版商)”最低求助积分说明 809021