p‐Coumaric acid decarboxylase from Lactobacillus plantarum: Structural insights into the active site and decarboxylation catalytic mechanism

Abstract

p-Coumaric acid decarboxylases (PDCs) catalyze the nonoxidative decarboxylation of hydroxycinnamic acids to generate the corresponding vinyl derivatives. Despite the biotechnological relevance of PDCs in food industry, their catalytic mechanism remains largely unknown. Here, we report insights into the structural basis of catalysis for the homodimeric PDC from Lactobacillus plantarum (LpPDC). The global fold of LpPDC is based on a flattened beta-barrel surrounding an internal cavity. Crystallographic and functional analyses of single-point mutants of residues located within this cavity have permitted identifying a potential substrate-binding pocket and also to provide structural evidences for rearrangements of surface loops so that they can modulate the accessibility to the active site. Finally, combination of the structural and functional data with in silico results enables us to propose a two-step catalytic mechanism for decarboxylation of p-coumaric acid by PDCs where Glu71 is involved in proton transfer, and Tyr18 and Tyr20 are involved in the proper substrate orientation and in the release of the CO(2) product.

Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae

“…Structural studies of phenol acid decarboxylases define the following three general types of this enzyme: (i) dodecameric, UbiXtype flavoproteins (23,24); (ii) the microbial lipocalin-related phenylacrylic acid decarboxylases (27)(28)(29); and (iii) the UbiD-like enzymes (30). The X-ray crystal structure of yeast FDC1 clearly establishes this enzyme as a member of the UbiD family of decarboxylases ( Fig.…”

“…In contrast to the dodecameric UbiX-like proteins, the phenolic acid decarboxylases from Lactobacillus plantarum, Bacillus pumilus, and Enterobacter sp. Px6-4 form a second class of enzymes that catalyze the nonoxidative decarboxylation of aromatic compounds (27)(28)(29). These enzymes are dimeric proteins, with each monomer (molecular mass, 19 to 22 kDa) adopting a flattened ␤-barrel architecture that shares structural homology with the lipocalin fold.…”

C−H Carboxylation of Aromatic Compounds through CO2 Fixation

“…)54 and salicylic acid decarboxylase (SAD Tm; Trichosporon moniliiforme )55 were also found to be efficient for the carboxylation process. The phenolic acid decarboxylase derived from Lactobacillus plantarum (PAD_Lp)56 and Bacillus amyloliquefaciens (PAD_Ba)57 selectively acted at the β‐carbon atom of styrenes forming ( E )‐cinnamic acids. Overall, this method for enzymatic carboxylation of phenols represents a promising biocatalytic equivalent to the classical Kolbe–Schmitt reaction to prepare the corresponding salicylic acid derivatives at low temperature and ambient pressure.…”

The Impact of Simple Phenolic Compounds on Beer Aroma and Flavor

“…The sequence of these enzymes reveals significant conservation across genera, and a structure and mechanism that does not require a known co-factor, unlike the S. cerevisiae PAD1/FDC1 system [54,57]. This group constitutes a PAD enzyme family that shares a flattened, compact beta-barrel structure, with the substrate binding site within the core of the barrel [57].…”