UbiD domain dynamics underpins aromatic decarboxylation

Stephen A. Marshall (), Karl A. P. Payne, Karl Fisher, Gabriel R. Titchiner, Colin Levy, Sam Hay and David Leys ()
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Stephen A. Marshall: University of Manchester
Karl A. P. Payne: University of Manchester
Karl Fisher: University of Manchester
Gabriel R. Titchiner: University of Manchester
Colin Levy: University of Manchester
Sam Hay: University of Manchester
David Leys: University of Manchester

Nature Communications, 2021, vol. 12, issue 1, 1-11

Abstract: Abstract The widespread UbiD enzyme family utilises the prFMN cofactor to achieve reversible decarboxylation of acrylic and (hetero)aromatic compounds. The reaction with acrylic compounds based on reversible 1,3-dipolar cycloaddition between substrate and prFMN occurs within the confines of the active site. In contrast, during aromatic acid decarboxylation, substantial rearrangement of the substrate aromatic moiety associated with covalent catalysis presents a molecular dynamic challenge. Here we determine the crystal structures of the multi-subunit vanillic acid decarboxylase VdcCD. We demonstrate that the small VdcD subunit acts as an allosteric activator of the UbiD-like VdcC. Comparison of distinct VdcCD structures reveals domain motion of the prFMN-binding domain directly affects active site architecture. Docking of substrate and prFMN-adduct species reveals active site reorganisation coupled to domain motion supports rearrangement of the substrate aromatic moiety. Together with kinetic solvent viscosity effects, this establishes prFMN covalent catalysis of aromatic (de)carboxylation is afforded by UbiD dynamics.

Date: 2021
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DOI: 10.1038/s41467-021-25278-z

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