A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase.
A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase.
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葡萄糖胺 6-磷酸脱氨酶中 pH 依赖性开环催化和盖基序灵活性的 QM/MM MD 研究。
DOI：
10.1039/c4cp01609b
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发表时间：
2014-08
影响因子：
3.3
通讯作者：
Cao, Zexing
中科院分区：
文献类型：
--
作者：
Zhao, Yuan;Chen, Nanhao;Wu, Ruibo;Cao, Zexing
The glucosamine 6-phosphate deaminase (NagB), which catalyzes the conversion of D-glucosamine 6-phosphate (GlcN6P) into d-fructose 6-phosphate (F6P) and ammonia, determines the final metabolic fate of N-acetylglucosamine (GlcNAc). Here using state-of-the-art ab initio QM/MM MD simulations, we have explored the plausible mechanisms for the enzymatic ring-opening of GlcN6P in the basic environment. Two different proton-shuttle mechanisms have been proposed. Calculations show that the protonated state of the amino group in the substrate dominates the concerted and stepwise catalytic pathways and a catalytic triad plays an important role in mediating the proton transfer and the resulting ring-opening process. The free energy barrier for the rate-determining step in the low-energy stepwise reaction is 17.9 kcal mol(-1). In acidic solution, the lid motif prefers a closed state while it always stays in the open state in basic solution upon substrate binding, which is basically dominated by the protonated state of the residue His145.
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影响因子：
15
作者：
Ke, Zhihong;Smith, Gregory K.;Zhang, Yingkai;Guo, Hua
通讯作者：
Guo, Hua
影响因子：
15
作者：
Ruibo Wu;Hujun Xie;Z. Cao;Y. Mo
通讯作者：
Ruibo Wu;Hujun Xie;Z. Cao;Y. Mo
影响因子：
3.5
作者：
V. Shevchenko;Mark Hogben;R. Ekong;J. Parrington;F. Lai
通讯作者：
V. Shevchenko;Mark Hogben;R. Ekong;J. Parrington;F. Lai
影响因子：
1.9
作者：
Cheon K;Moser SA;Wiener HW;Whiddon J;Momeni SS;Ruby JD;Cutter GR;Childers NK
通讯作者：
Childers NK
DOI：
10.1107/s0907444901016699
发表时间：
2002
期刊：
Acta crystallographica. Section D, Biological crystallography
影响因子：
--
作者：
E. Rudiño-Piñera;S. Morales-Arrieta;S. Rojas-Trejo;E. Horjales
通讯作者：
E. Rudiño-Piñera;S. Morales-Arrieta;S. Rojas-Trejo;E. Horjales