UbiD domain dynamics underpins aromatic decarboxylation

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.

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Fig: Mechanism and structures of the UbiD enzyme family: a Proposed 1,3 dipolar cycloaddition Fdc1 mechanism16,17. b A substrate nucleophilic attack mechanism proposed for phenolic substrates18. cElectrophilic aromatic substitution mechanism postulated for PA0254-mediated decarboxylation of pyrrole-2-carboxylate19. All mechanisms share a common Int2 intermediate with an sp2 hybridized substrate Cα. Transient dearomatisation occurring for Int1 and Int3 species presents a significant energy barrier in each case. prFMN-R = phosphoribityl moiety (omitted for clarity) d Overlay of UbiD monomers anchored on the prFMN binding domain (in blue). The oligomerisation domains of Fdc and PA0254 are shown in orange (representing a closed conformation), while UbiD, HmfF and AroY are shown in open states (in red). The C-terminal helix is shown in grey. The hinge region is located within a helix (in green) connecting the oligomerisation and prFMN binding domains, close to bound cofactor (in yellow spheres).

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.

Marshall, S.A., Payne, K.A.P., Fisher, K. et al. UbiD domain dynamics underpins aromatic decarboxylation. Nat Commun 12, 5065 (2021). https://doi.org/10.1038/s41467-021-25278-z

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