Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI

	Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI
	Zhang, Shujun 1; Ma, Guangcai 1; Liu, Yongjun 1,2; Ling, Baoping 3
刊名	journal of molecular graphics & modelling
	2015-09-01
卷号	61 页码:21-29
关键词	2-Pyrone-4,6-dicarboxylate lactonase LigI 2-Pyrone-4,6-dicarboxylate (PDC) QM/MM Hydrolysis mechanism
中文摘要	2-pyrone-4,6-dicarboxylate lactonase (ligi) is the first identified enzyme from amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity. it catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (pdc) to 4-oxalomesaconate (oma) and 4-carboxy-2-hydroxymuconate (chm) in the degradation of lignin. in this paper, a combined quantum mechanics and molecule mechanics (qm/mm) approach was employed to study the reaction mechanism of ligi from sphingomonas paucimobilis. according to the results of our calculations, the whole catalytic reaction contains three elementary steps, including the nucleophilic attack, the cleavage of c-o of lactone (substrate) and the intramolecular proton transfer. the intermediate has two intramolecular proton transfer pathways, due to which, two final hydrolysis products can be obtained. the energy profile indicates that 4-carboxy-2-hydroxymuconate (chm) is the main hydrolysis product, therefore, the isomerization between 4-carboxy-2-hydroxymuconate (chm) and 4-oxalomesaconate (oma) is suggested to occur in solvent. during the catalytic reaction, residue asp248 acts as a general base to activate the hydrolytic water molecule. although his31, his33 and his180 do not directly participate in the chemical process, they play assistant roles by forming electrostatic interactions with the substrate and its involved species in activating the carbonyl group of the substrate and stabilizing the intermediates and transition states. (c) 2015 elsevier inc. all rights reserved.
英文摘要	2-pyrone-4,6-dicarboxylate lactonase (ligi) is the first identified enzyme from amidohydrolase superfamily that does not require a divalent metal ion for catalytic activity. it catalyzes the reversible hydrolysis of 2-pyrone-4,6-dicarboxylate (pdc) to 4-oxalomesaconate (oma) and 4-carboxy-2-hydroxymuconate (chm) in the degradation of lignin. in this paper, a combined quantum mechanics and molecule mechanics (qm/mm) approach was employed to study the reaction mechanism of ligi from sphingomonas paucimobilis. according to the results of our calculations, the whole catalytic reaction contains three elementary steps, including the nucleophilic attack, the cleavage of c-o of lactone (substrate) and the intramolecular proton transfer. the intermediate has two intramolecular proton transfer pathways, due to which, two final hydrolysis products can be obtained. the energy profile indicates that 4-carboxy-2-hydroxymuconate (chm) is the main hydrolysis product, therefore, the isomerization between 4-carboxy-2-hydroxymuconate (chm) and 4-oxalomesaconate (oma) is suggested to occur in solvent. during the catalytic reaction, residue asp248 acts as a general base to activate the hydrolytic water molecule. although his31, his33 and his180 do not directly participate in the chemical process, they play assistant roles by forming electrostatic interactions with the substrate and its involved species in activating the carbonyl group of the substrate and stabilizing the intermediates and transition states. (c) 2015 elsevier inc. all rights reserved.
WOS标题词	science & technology ; life sciences & biomedicine ; technology ; physical sciences
类目[WOS]	biochemical research methods ; biochemistry & molecular biology ; computer science, interdisciplinary applications ; crystallography ; mathematical & computational biology
研究领域[WOS]	biochemistry & molecular biology ; computer science ; crystallography ; mathematical & computational biology
关键词[WOS]	sphingomonas-paucimobilis syk-6 ; molecular-dynamics ; amidohydrolase superfamily ; dispersion correction ; manganese peroxidase ; lignin degradation ; acid pdc ; qm/mm ; energy ; phosphotriesterase
收录类别	SCI
语种	英语
WOS记录号	WOS:000362137500003
内容类型	期刊论文
源URL	[http://ir.nwipb.ac.cn/handle/363003/5513]
专题	西北高原生物研究所_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, Key Lab Tibetan Med Res, Xining 810001, Qinghai, Peoples R China 3.Qufu Normal Univ, Sch Chem & Chem Engn, Qufu 273165, Shandong, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Shujun,Ma, Guangcai,Liu, Yongjun,et al. Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI[J]. journal of molecular graphics & modelling,2015,61:21-29.
APA	Zhang, Shujun,Ma, Guangcai,Liu, Yongjun,&Ling, Baoping.(2015).Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI.journal of molecular graphics & modelling,61,21-29.
MLA	Zhang, Shujun,et al."Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI".journal of molecular graphics & modelling 61(2015):21-29.