6EV8

Structure of E277Q A. niger Fdc1 with prFMN in the hydroxylated form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.146 

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-Arg-Glu/Asp ionic network in the enzym ...

    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 ketimine and prFMN iminium , have been observed. It also has been suggested that only the prFMN iminium 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 prFMN iminium to prFMN ketimine is a light-dependent process that is largely independent of the Glu 277 -Arg 173 -Glu 282 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 iminium 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.


    Organizational Affiliation

    From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and david.leys@manchester.ac.uk.,From the Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, M1 7DN, United Kingdom and.,Innovation/Biodomain, Shell International Exploration and Production, Westhollow Technology Center, Houston, Texas 77082-3101.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferulic acid decarboxylase 1
A
508Aspergillus niger (strain CBS 513.88 / FGSC A1513)Mutation(s): 0 
Gene Names: fdc1
EC: 4.1.1.102
Find proteins for A2QHE5 (Aspergillus niger (strain CBS 513.88 / FGSC A1513))
Go to UniProtKB:  A2QHE5
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

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

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Download CCD File 
A
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
SCN
Query on SCN

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Download CCD File 
A
THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M
 Ligand Interaction
BYN
Query on BYN

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Download CCD File 
A
hydroxylated prenyl-FMN
C22 H31 N4 O10 P
BDNVCRCOZIAGID-LWGWVAHUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.03 Å
  • R-Value Free: 0.165 
  • R-Value Work: 0.146 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.910α = 90.00
b = 63.810β = 90.00
c = 87.750γ = 90.00
Software Package:
Software NamePurpose
iMOSFLMdata reduction
xia2data scaling
REFMACrefinement
REFMACphasing

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