title: Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae.
abstract: The nonoxidative decarboxylation of aromatic acids occurs in a range of microbes and is of interest for bioprocessing and metabolic engineering. Although phenolic acid decarboxylases provide useful tools for bioindustrial applications, the molecular bases for how these enzymes function are only beginning to be examined. Here we present the 2.35-Å-resolution X-ray crystal structure of the ferulic acid decarboxylase (FDC1; UbiD) from Saccharomyces cerevisiae. FDC1 shares structural similarity with the UbiD family of enzymes that are involved in ubiquinone biosynthesis. The position of 4-vinylphenol, the product of p-coumaric acid decarboxylation, in the structure identifies a large hydrophobic cavity as the active site. Differences in the β2e-α5 loop of chains in the crystal structure suggest that the conformational flexibility of this loop allows access to the active site. The structure also implicates Glu285 as the general base in the nonoxidative decarboxylation reaction catalyzed by FDC1. Biochemical analysis showed a loss of enzymatic activity in the E285A mutant. Modeling of 3-methoxy-4-hydroxy-5-decaprenylbenzoate, a partial structure of the physiological UbiD substrate, in the binding site suggests that an ∼30-Å-long pocket adjacent to the catalytic site may accommodate the isoprenoid tail of the substrate needed for ubiquinone biosynthesis in yeast. The three-dimensional structure of yeast FDC1 provides a template for guiding protein engineering studies aimed at optimizing the efficiency of aromatic acid decarboxylation reactions in bioindustrial applications.
authors: Conagen, Inc., Bedford, Massachusetts, USA.
authors: Mohammad Wadud
authors: MW
authors: Bhuiya
authors: Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.
authors: Soon Goo
authors: SG
authors: Lee
authors: Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA jjez@wustl.edu oliver.yu@conagen-inc.com.
authors: Joseph M
authors: JM
authors: Jez
authors: Conagen, Inc., Bedford, Massachusetts, USA Wuxi NewWay, Wuxi, Jiangsu, China jjez@wustl.edu oliver.yu@conagen-inc.com.
authors: Oliver
authors: O
authors: Yu
mesh_terms: D000595:Amino Acid Sequence; D002262:Carboxy-Lyases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020134:Catalytic Domain; D003373:Coumaric Acids / Q000378:metabolism; D018360:Crystallography, X-Ray; D003653:Decarboxylation; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D010636:Phenols / Q000378:metabolism; D011422:Propionates; D011487:Protein Conformation; D054730:Protein Interaction Domains and Motifs; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000235:genetics; D016415:Sequence Alignment; D014451:Ubiquinone / Q000096:biosynthesis
chemical_list: D003373:Coumaric Acids; D010636:Phenols; D011422:Propionates; D014451:Ubiquinone; D002262:Carboxy-Lyases; C087194:phenylacrylic acid decarboxylase; C495469:p-coumaric acid; C030626:4-vinylphenol