6EVF

Structure of E285D S. cerevisiae Fdc1 with prFMN in the hydroxylated form

Summary for 6EVF

• Entry DOI: 10.2210/pdb6evf/pdb
• Descriptor: Ferulic acid decarboxylase 1, 1-deoxy-5-O-phosphono-1-(3,3,4,5-tetramethyl-9,11-dioxo-2,3,8,9,10,11-hexahydro-7H-quinolino[1,8-fg]pteridin-12-ium-7-y l)-D-ribitol, MANGANESE (II) ION, ... (5 entities in total)
• Functional Keywords: lyase
• Biological source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
• Cellular location: Cytoplasm : Q03034
• Total number of polymer chains: 4
• Total formula weight: 230664.16

Authors

Bailey, S.S.,David, L.,Payne, K.A.P. (deposition date: 2017-11-01, release date: 2017-12-20, Last modification date: 2024-01-17)

Primary citation

Bailey, S.S.,Payne, K.A.P.,Fisher, K.,Marshall, S.A.,Cliff, M.J.,Spiess, R.,Parker, D.A.,Rigby, S.E.J.,Leys, D.
The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis.
J. Biol. Chem., 293:2272-2287, 2018

PubMed 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 and prFMN, have been observed. It also has been suggested that only the prFMN form is relevant to catalysis, which requires transient cycloaddition between substrate and cofactor. Using Fdc1 as a model system, we reveal that isomerization of prFMN to prFMN is a light-dependent process that is largely independent of the Glu-Arg-Glu 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 prFMN 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.

PubMed: 29259125
DOI: 10.1074/jbc.RA117.000881

Experimental method

X-RAY DIFFRACTION (2.06 Å)