A QM/MM study of the catalytic mechanism of nicotinamidase

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	A QM/MM study of the catalytic mechanism of nicotinamidase
	Sheng, Xiang 1; Liu, Yongjun 1,2
	2014
发表期刊	ORGANIC & BIOMOLECULAR CHEMISTRY
ISSN	1477-0520
卷号	12 期号:8 页码:1265-1277
文章类型	Article
摘要	Nicotinamidase (Pnc1) is a member of Zn-dependent amidohydrolases that hydrolyzes nicotinamide (NAM) to nicotinic acid (NA), which is a key step in the salvage pathway of NAD(+) biosynthesis. In this paper, the catalytic mechanism of Pnc1 has been investigated by using a combined quantum-mechanical/molecular-mechanical (QM/MM) approach based on the recently obtained crystal structure of Pnc1. The reaction pathway, the detail of each elementary step, the energetics of the whole catalytic cycle, and the roles of key residues and Zn-binding site are illuminated. Our calculation results indicate that the catalytic water molecule comes from the bulk solvent, which is then deprotonated by residue D8. D8 functions as a proton transfer station between C167 and NAM, while the activated C167 serves as the nucleophile. The residue K122 only plays a role in stabilizing intermediates and transition states. The oxyanion hole formed by the amide backbone nitrogen atoms of A163 and C167 has the function to stabilize the hydroxyl anion of nicotinamide. The Zn-binding site rather than a single Zn2+ ion acts as a Lewis acid to influence the reaction. Two elementary steps, the activation of C167 in the deamination process and the decomposition of catalytic water in the hydrolysis process, correspond to the large energy barriers of 25.7 and 28.1 kcal mol(-1), respectively, meaning that both of them contribute a lot to the overall reaction barrier. Our results may provide useful information for the design of novel and efficient Pnc1 inhibitors and related biocatalytic applications.; Nicotinamidase (Pnc1) is a member of Zn-dependent amidohydrolases that hydrolyzes nicotinamide (NAM) to nicotinic acid (NA), which is a key step in the salvage pathway of NAD(+) biosynthesis. In this paper, the catalytic mechanism of Pnc1 has been investigated by using a combined quantum-mechanical/molecular-mechanical (QM/MM) approach based on the recently obtained crystal structure of Pnc1. The reaction pathway, the detail of each elementary step, the energetics of the whole catalytic cycle, and the roles of key residues and Zn-binding site are illuminated. Our calculation results indicate that the catalytic water molecule comes from the bulk solvent, which is then deprotonated by residue D8. D8 functions as a proton transfer station between C167 and NAM, while the activated C167 serves as the nucleophile. The residue K122 only plays a role in stabilizing intermediates and transition states. The oxyanion hole formed by the amide backbone nitrogen atoms of A163 and C167 has the function to stabilize the hydroxyl anion of nicotinamide. The Zn-binding site rather than a single Zn2+ ion acts as a Lewis acid to influence the reaction. Two elementary steps, the activation of C167 in the deamination process and the decomposition of catalytic water in the hydrolysis process, correspond to the large energy barriers of 25.7 and 28.1 kcal mol(-1), respectively, meaning that both of them contribute a lot to the overall reaction barrier. Our results may provide useful information for the design of novel and efficient Pnc1 inhibitors and related biocatalytic applications.
WOS标题词	Science & Technology ; Physical Sciences
关键词[WOS]	MOLECULAR-DYNAMICS SIMULATIONS ; MYCOBACTERIUM-TUBERCULOSIS ; SACCHAROMYCES-CEREVISIAE ; ADENINE-DINUCLEOTIDE ; ENZYMATIC-REACTIONS ; CRYSTAL-STRUCTURE ; TRANSITION-STATE ; METAL-IONS ; PYRAZINAMIDASE ; INHIBITION
收录类别	SCI
语种	英语
WOS研究方向	Chemistry
WOS类目	Chemistry, Organic
WOS记录号	WOS:000330792500013
引用统计	被引频次：12[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/4285
专题	中国科学院西北高原生物研究所
作者单位	1.Shandong Univ, Sch Chem & Chem Engn, Jinan 250100, Shandong, Peoples R China 2.Chinese Acad Sci, Northwest Inst Plateau Biol, Xining 810001, Qinghai, Peoples R China
推荐引用方式 GB/T 7714	Sheng, Xiang,Liu, Yongjun. A QM/MM study of the catalytic mechanism of nicotinamidase[J]. ORGANIC & BIOMOLECULAR CHEMISTRY,2014,12(8):1265-1277.
APA	Sheng, Xiang,&Liu, Yongjun.(2014).A QM/MM study of the catalytic mechanism of nicotinamidase.ORGANIC & BIOMOLECULAR CHEMISTRY,12(8),1265-1277.
MLA	Sheng, Xiang,et al."A QM/MM study of the catalytic mechanism of nicotinamidase".ORGANIC & BIOMOLECULAR CHEMISTRY 12.8(2014):1265-1277.

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