6EVE

Structure of R175A S. cerevisiae Fdc1 with prFMN in the iminium form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

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

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.

(2018) J. Biol. Chem. 293: 2272-2287

  • DOI: 10.1074/jbc.RA117.000881
  • Primary Citation of Related Structures:  

  • 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-ArgGlu/Asp ionic network in the enzyme ...

    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-ArgGlu/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 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-Ar-Glu network, as only Glu to 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 likely 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.


    Organizational Affiliation

    The University of Manchester, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferulic acid decarboxylase 1
A, B, C, D
509Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 1 
Gene Names: FDC1
EC: 4.1.1.102
Find proteins for Q03034 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03034
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B, C
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
4LU
Query on 4LU

Download SDF File 
Download CCD File 
A, B, C, D
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-yl)-D-ribitol
prenylated-FMN iminium form
C22 H30 N4 O9 P
KOUJZPGFPGLHCZ-IYOUNJFTSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 117.480α = 90.00
b = 98.640β = 97.24
c = 118.170γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
REFMACphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited Kingdom--

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references
  • Version 1.2: 2018-01-03
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Author supporting evidence
  • Version 1.4: 2018-02-28
    Type: Database references