6EVD

Structure of R173A A. niger Fdc1 with prFMN in the hydroxylated form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 

Starting Model: experimental
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This is version 1.5 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: https://doi.org/10.1074/jbc.RA117.000881
  • Primary Citation of Related Structures:  
    6EV3, 6EV4, 6EV5, 6EV6, 6EV7, 6EV8, 6EV9, 6EVA, 6EVB, 6EVC, 6EVD, 6EVE, 6EVF

  • 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 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1508Aspergillus niger CBS 513.88Mutation(s): 0 
Gene Names: fdc1An03g06590
EC: 4.1.1.102
UniProt
Find proteins for A2QHE5 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513))
Explore A2QHE5 
Go to UniProtKB:  A2QHE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA2QHE5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.19 Å
  • R-Value Free: 0.162 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.145 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.23α = 90
b = 64.11β = 90
c = 87.44γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2017-12-27
    Changes: Database references
  • Version 1.2: 2018-01-03
    Changes: Database references
  • Version 1.3: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.4: 2018-02-28
    Changes: Database references
  • Version 1.5: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description