Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

作     者：Rodrigues, Andria V. Moriarty, Nigel W. Kakumanu, Ramu DeGiovanni, Andy Pereira, Jose Henrique Gin, Jennifer W. Chen, Yan Baidoo, Edward E. K. Petzold, Christopher J. Adams, Paul D. 

作者机构：Joint BioEnergy Inst Emeryville CA 94608 USA Lawrence Berkeley Natl Lab Mol Biophys & Integrated Bioimaging Berkeley CA 94720 USA Lawrence Berkeley Natl Lab Biol Syst & Engn Div Berkeley CA USA Dept Energy Agile BioFoundry Emeryville CA USA Univ Calif Berkeley Dept Bioengn Berkeley CA 94720 USA 

出 版 物：《JOURNAL OF BIOLOGICAL CHEMISTRY》 (生物化学杂志)

年 卷 期：2024年第300卷第10期

页      面：107736-107736页

核心收录：

学科分类：0710[理学-生物学] 071010[理学-生物化学与分子生物学] 07[理学] 

基　　金：US National Institutes of Health [P01GM063210] Phenix Industrial Consortium Agile BioFoundry [DE-AC02-05CH11231] 

主　　题：NADP oxidoreductase lignin degradation polymer synthesis pyrone 2 4 dicarboxylic acid enzyme catalysis structure-function crystal structure alphafold ligand docking computational modeling 

摘      要：Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme s mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.