The UbiD superfamily of enzymes are reversible decarboxylases that depend on the novel cofactor prenylated FMN (prFMN) for activity. The partner protein UbiX prenylates FMNH2 using dimethylallyl phosphate. The UbiX product, prFMNH2 is then passed to UbiD, where oxidative maturation to an active form, prFMNiminium occurs. Following oxidative activation, UbiD family members are able to catalyse the reversible decarboxylation of a wide range of unsaturated aliphatic and aromatic acids. The UbiD family contain a conserved active site E(D)RE motif that is proposed to play a role in cofactor maturation and decarboxylation. The Fdc1 enzyme from Aspergillus niger catalyses the decarboxylation of cinnamic acid and acts as a model system for studying UbiD enzymes, due to its amenability to high resolution crystallographic studies, ease of purification and readily detectable decarboxylation activity. Our studies on Fdc1 provide valuable insights into the role of the conserved ERE motif in cofactor maturation, isomerisation, and substrate (de)carboxylation. We confirm prFMNiminium is the active form, with illumination leading to inactivation through formation of the prFMNketimine isomer. We demonstrate ERE predominantly acts in catalysis, but not maturation or isomerisation. Our crystallographic studies of Fdc1 in complex with alkene substrates and alkyne inhibitors provides the first direct evidence for enzymatic 1,3-dipolar cycloaddition. These crystal structures also demonstrate a crucial role for molecular strain, whereby the enzyme is able to achieve reversible cycloaddition through selective destabilisation of key intermediates. Hence, we present strong evidence for the proposed 1,3-dipolar cycloaddition mechanism in case of enoic acid substrates. This leads to the question whether a similar mechanism also applies in case of aromatic acids, as occurs in distinct branches of the UbiD family. This remains a contentious issue, and will require future studies on distinct representatives of the UbiD-superfamily.