The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis

J Biol Chem. 2018 Feb 16;293(7):2272-2287. doi: 10.1074/jbc.RA117.000881. Epub 2017 Dec 19.


The UbiD family of reversible decarboxylases act on aromatic, heteroaromatic, and unsaturated aliphatic acids and utilize a prenylated flavin mononucleotide (prFMN) as cofactor, bound adjacent to a conserved Glu-Arg-Glu/Asp ionic network in the enzyme's active site. It is proposed that UbiD activation requires oxidative maturation of the cofactor, for which two distinct isomers, prFMNketimine and prFMNiminium, have been observed. It also has been suggested that only the prFMNiminium form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Aspergillus niger Fdc1 as a model system, we reveal that isomerization of prFMNiminium to prFMNketimine is a light-dependent process that is largely independent of the Glu277-Arg173-Glu282 network and accompanied by irreversible loss of activity. On the other hand, efficient catalysis was highly dependent on an intact Glu-Arg-Glu network, as only Glu → Asp substitutions retain activity. Surprisingly, oxidative maturation to form the prFMNiminium species is severely affected only for the R173A variant. In summary, the unusual irreversible isomerization of prFMN is light-dependent and probably proceeds via high-energy intermediates but is independent of the Glu-Arg-Glu network. Our results from mutagenesis, crystallographic, spectroscopic, and kinetic experiments indicate a clear role for the Glu-Arg-Glu network in both catalysis and oxidative maturation.

Keywords: EPR; UbiD; crystal structure; decarboxylase; enzyme catalysis; enzyme mechanism; enzyme structure; flavin; oxidation-reduction (redox); prenylated flavin mononucleotide (prFMN); radical.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aspergillus niger / chemistry
  • Aspergillus niger / enzymology*
  • Aspergillus niger / genetics
  • Binding Sites
  • Carboxy-Lyases / chemistry*
  • Carboxy-Lyases / genetics
  • Carboxy-Lyases / metabolism*
  • Catalysis
  • Catalytic Domain
  • Conserved Sequence
  • Flavin Mononucleotide / chemistry
  • Flavin Mononucleotide / metabolism*
  • Fungal Proteins / chemistry*
  • Fungal Proteins / genetics
  • Fungal Proteins / metabolism*
  • Isomerism
  • Kinetics
  • Oxidation-Reduction


  • Fungal Proteins
  • Flavin Mononucleotide
  • Carboxy-Lyases