Knowledge Management System of Northwest Institute of Plateau Biology, CAS
| Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI | |
| Zhang, Shujun1; Ma, Guangcai1; Liu, Yongjun1,2; Ling, Baoping3 | |
| 2015-09-01 | |
| 发表期刊 | JOURNAL OF MOLECULAR GRAPHICS & MODELLING
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| 卷号 | 61页码:21-29 |
| 文章类型 | Article |
| 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.; 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. |
| 关键词 | Ligi 2-pyrone-4 6-dicarboxylate Lactonase Qm/mm 2-pyrone-4 Hydrolysis Mechanism 6-dicarboxylate (Pdc) |
| WOS标题词 | Science & Technology ; Life Sciences & Biomedicine ; Technology ; Physical Sciences |
| 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研究方向 | Biochemistry & Molecular Biology ; Computer Science ; Crystallography ; Mathematical & Computational Biology |
| WOS类目 | Biochemical Research Methods ; Biochemistry & Molecular Biology ; Computer Science, Interdisciplinary Applications ; Crystallography ; Mathematical & Computational Biology |
| WOS记录号 | WOS:000362137500003 |
| 引用统计 | |
| 文献类型 | 期刊论文 |
| 条目标识符 | http://210.75.249.4/handle/363003/5513 |
| 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, 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. |
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