PDBsum entry 6evd

Lyase

PDB id: 6evd

Contents

Protein chain

496 a.a.

Ligands

BYN

Metals

_MN

__K

Waters ×782

References listed in PDB file

Key reference

• Title: The role of conserved residues in fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, Cofactor isomerization, And catalysis.
• Authors: S.S.Bailey, K.A.P.Payne, K.Fisher, S.A.Marshall, M.J.Cliff, R.Spiess, D.A.Parker, S.E.J.Rigby, D.Leys.
• Ref.: J Biol Chem, 2018, 293, 2272-2287.
• PubMed id: 29259125

Abstract

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, prFMN^ketimineand prFMN^iminium, have been observed. It also has been suggested that only the prFMN^iminiumform is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. UsingAspergillus nigerFdc1 as a model system, we reveal that isomerization of prFMN^iminiumto prFMN^ketimineis a light-dependent process that is largely independent of the Glu²⁷⁷-Arg¹⁷³-Glu²⁸²network 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 prFMN^iminiumspecies 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.