A QM/MM study of the catalytic mechanism of nicotinamidase

NWIPB OpenIR

	A QM/MM study of the catalytic mechanism of nicotinamidase
	Sheng, Xiang ; Liu, Yongjun
	2014
发表期刊	ORGANIC & BIOMOLECULAR CHEMISTRY ; Sheng, X; Liu, YJ.A QM/MM study of the catalytic mechanism of nicotinamidase,ORGANIC & BIOMOLECULAR CHEMISTRY,2014,12(8):1265
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.
文献类型	期刊论文
条目标识符	http://210.75.249.4/handle/363003/37437
专题	中国科学院西北高原生物研究所
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, Sheng, X; Liu, YJ.A QM/MM study of the catalytic mechanism of nicotinamidase,ORGANIC & BIOMOLECULAR CHEMISTRY,2014,12(8):1265,2014.
APA	Sheng, Xiang,&Liu, Yongjun.(2014).A QM/MM study of the catalytic mechanism of nicotinamidase.ORGANIC & BIOMOLECULAR CHEMISTRY.
MLA	Sheng, Xiang,et al."A QM/MM study of the catalytic mechanism of nicotinamidase".ORGANIC & BIOMOLECULAR CHEMISTRY (2014).