PDBsum entry 6evd

Lyase

PDB id: 6evd

Contents

Protein chain

496 a.a.

Ligands

BYN

Metals

_MN

__K

Waters ×782

PDB id:

6evd

Name:

Lyase

Title:

Structure of r173a a. Niger fdc1 with prfmn in the hydroxylated form

Structure:

Ferulic acid decarboxylase 1. Chain: a. Synonym: phenacrylate decarboxylase. Engineered: yes

Source:

Aspergillus niger (strain cbs 513.88 / fgsc a1513). Organism_taxid: 425011. Strain: cbs 513.88 / fgsc a1513. Gene: fdc1, an03g06590. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008

Resolution:

1.19Å R-factor: 0.145 R-free: 0.162

Authors:

S.S.Bailey,L.David,K.A.P.Payne

Key ref:

S.S.Bailey et al. (2018). The role of conserved residues in Fdc decarboxylase in prenylated flavin mononucleotide oxidative maturation, cofactor isomerization, and catalysis. J Biol Chem, 293, 2272-2287. PubMed id: 29259125

Date:

01-Nov-17 Release date: 20-Dec-17

Protein chain

A2QHE5  (FDC1_ASPNC) -  Ferulic acid decarboxylase 1 from Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)

Seq: 500 a.a.

Struc: 496 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.4.1.1.102 - phenacrylate decarboxylase.
• Reaction:
  1. (E)-4-coumarate + H⁺ = 4-vinylphenol + CO2
  2. (E)-cinnamate + H⁺ = styrene + CO2
  3. (E)-ferulate + H⁺ = 2-methoxy-4-vinylphenol + CO2
• Cofactor: Prenyl-FMNH(2)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

J Biol Chem 293:2272-2287 (2018)

PubMed id: 29259125

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

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.

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.