4S13

Ferulic Acid Decarboxylase (FDC1)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.348 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and Mechanism of Ferulic Acid Decarboxylase (FDC1) from Saccharomyces cerevisiae.

Bhuiya, M.W.Lee, S.G.Jez, J.M.Yu, O.

(2015) Appl.Environ.Microbiol. 81: 4216-4223

  • DOI: 10.1128/AEM.00762-15

  • PubMed Abstract: 
  • The nonoxidative decarboxylation of aromatic acids occurs in a range of microbes and is of interest for bioprocessing and metabolic engineering. Although phenolic acid decarboxylases provide useful tools for bioindustrial applications, the molecular ...

    The nonoxidative decarboxylation of aromatic acids occurs in a range of microbes and is of interest for bioprocessing and metabolic engineering. Although phenolic acid decarboxylases provide useful tools for bioindustrial applications, the molecular bases for how these enzymes function are only beginning to be examined. Here we present the 2.35-Å-resolution X-ray crystal structure of the ferulic acid decarboxylase (FDC1; UbiD) from Saccharomyces cerevisiae. FDC1 shares structural similarity with the UbiD family of enzymes that are involved in ubiquinone biosynthesis. The position of 4-vinylphenol, the product of p-coumaric acid decarboxylation, in the structure identifies a large hydrophobic cavity as the active site. Differences in the β2e-α5 loop of chains in the crystal structure suggest that the conformational flexibility of this loop allows access to the active site. The structure also implicates Glu285 as the general base in the nonoxidative decarboxylation reaction catalyzed by FDC1. Biochemical analysis showed a loss of enzymatic activity in the E285A mutant. Modeling of 3-methoxy-4-hydroxy-5-decaprenylbenzoate, a partial structure of the physiological UbiD substrate, in the binding site suggests that an ∼30-Å-long pocket adjacent to the catalytic site may accommodate the isoprenoid tail of the substrate needed for ubiquinone biosynthesis in yeast. The three-dimensional structure of yeast FDC1 provides a template for guiding protein engineering studies aimed at optimizing the efficiency of aromatic acid decarboxylation reactions in bioindustrial applications.


    Organizational Affiliation

    Conagen, Inc., Bedford, Massachusetts, USA.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA.,Conagen, Inc., Bedford, Massachusetts, USA Wuxi NewWay, Wuxi, Jiangsu, China jjez@wustl.edu oliver.yu@conagen-inc.com.,Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA jjez@wustl.edu oliver.yu@conagen-inc.com.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ferulic acid decarboxylase 1
A, B, C, D, E, F, G, H
503Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4VP
Query on 4VP

Download SDF File 
Download CCD File 
A, C, E, F, G
4-ethenylphenol
C8 H8 O
FUGYGGDSWSUORM-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.348 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.171 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 251.963α = 90.00
b = 120.995β = 121.93
c = 159.560γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data collection
HKL-3000data scaling
PHENIXrefinement
SCALEPACKdata scaling
HKL-3000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-05-06
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references