4ZAC

Structure of S. cerevisiae Fdc1 with the prenylated-flavin cofactor in the iminium form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

New cofactor supports alpha , beta-unsaturated acid decarboxylation via 1,3-dipolar cycloaddition.

Payne, K.A.White, M.D.Fisher, K.Khara, B.Bailey, S.S.Parker, D.Rattray, N.J.Trivedi, D.K.Goodacre, R.Beveridge, R.Barran, P.Rigby, S.E.Scrutton, N.S.Hay, S.Leys, D.

(2015) Nature 522: 502-506

  • DOI: 10.1038/nature14560
  • Primary Citation of Related Structures:  
    4ZA4, 4ZA5, 4ZA7, 4ZA8, 4ZA9, 4ZAC, 4ZAD, 4ZAA, 4ZAB

  • PubMed Abstract: 
  • The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthe ...

    The bacterial ubiD and ubiX or the homologous fungal fdc1 and pad1 genes have been implicated in the non-oxidative reversible decarboxylation of aromatic substrates, and play a pivotal role in bacterial ubiquinone (also known as coenzyme Q) biosynthesis or microbial biodegradation of aromatic compounds, respectively. Despite biochemical studies on individual gene products, the composition and cofactor requirement of the enzyme responsible for in vivo decarboxylase activity remained unclear. Here we show that Fdc1 is solely responsible for the reversible decarboxylase activity, and that it requires a new type of cofactor: a prenylated flavin synthesized by the associated UbiX/Pad1. Atomic resolution crystal structures reveal that two distinct isomers of the oxidized cofactor can be observed, an isoalloxazine N5-iminium adduct and a N5 secondary ketimine species with markedly altered ring structure, both having azomethine ylide character. Substrate binding positions the dipolarophile enoic acid group directly above the azomethine ylide group. The structure of a covalent inhibitor-cofactor adduct suggests that 1,3-dipolar cycloaddition chemistry supports reversible decarboxylation in these enzymes. Although 1,3-dipolar cycloaddition is commonly used in organic chemistry, we propose that this presents the first example, to our knowledge, of an enzymatic 1,3-dipolar cycloaddition reaction. Our model for Fdc1/UbiD catalysis offers new routes in alkene hydrocarbon production or aryl (de)carboxylation.


    Organizational Affiliation

    Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ferulic acid decarboxylase 1ABCD503Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FDC1YDR539WD3703.2
EC: 4.1.1 (PDB Primary Data), 4.1.1.102 (UniProt)
Find proteins for Q03034 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q03034 
Go to UniProtKB:  Q03034
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4LU
Query on 4LU

Download Ideal Coordinates 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-y l)-D-ribitol
C22 H30 N4 O9 P
KOUJZPGFPGLHCZ-IYOUNJFTSA-O
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
A, B, C, D
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
A, B, C, D
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.192 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.164 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.41α = 90
b = 96.18β = 96.58
c = 116.64γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-04-13 
  • Released Date: 2015-06-17 
  • Deposition Author(s): White, M.D., Leys, D.

Revision History 

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references
  • Version 1.2: 2019-02-20
    Changes: Data collection, Derived calculations
  • Version 1.3: 2019-07-10
    Changes: Data collection