title: Theoretical study of the hydrolysis mechanism of 2-pyrone-4,6-dicarboxylate (PDC) catalyzed by LigI.
abstract: 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 CO 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.
authors.affiliation: School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
authors.forename: Shujun
authors.initials: S
authors.lastname: Zhang
authors.affiliation: School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China.
authors.forename: Guangcai
authors.initials: G
authors.lastname: Ma
authors.affiliation: School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China; Key Laboratory of Tibetan Medicine Research, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, Qinghai 810001, China. Electronic address: yongjunliu_1@sdu.edu.cn.
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Liu
authors.affiliation: School of Chemistry and Chemical Engineering, Qufu Normal University, Qufu, Shandong 273165, China.
authors.forename: Baoping
authors.initials: B
authors.lastname: Ling
mesh_terms: D020816:Amino Acid Motifs; D001426:Bacterial Proteins / Q000737:chemistry*; D055162:Biocatalysis; D002265:Carboxylic Ester Hydrolases / Q000737:chemistry*; D006868:Hydrolysis; D008031:Lignin / Q000737:chemistry*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D011753:Pyrones / Q000737:chemistry*; D011789:Quantum Theory; D020578:Sphingomonas / Q000737:chemistry / Q000201:enzymology; D013379:Substrate Specificity
chemical_list: D001426:Bacterial Proteins; D011753:Pyrones; C024153:alpha-pyrone-4,6-dicarboxylic acid; D008031:Lignin; C036528:2-pyrone-4,6-dicarboxylic acid hydrolase; D002265:Carboxylic Ester Hydrolases
keywords: 2-Pyrone-4,6-dicarboxylate (PDC); 2-Pyrone-4,6-dicarboxylate lactonase; Hydrolysis mechanism; LigI; QM/MM