Structure of C. dubliensis Fdc1 with the prenylated-flavin cofactor in the iminium form.

Experimental Data Snapshot

  • Resolution: 2.46 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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

  • 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) 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
513Candida dubliniensisMutation(s): 0 
Gene Names: CD36_64160
Find proteins for B9WJ66 (Candida dubliniensis (strain CD36 / ATCC MYA-646 / CBS 7987 / NCPF 3949 / NRRL Y-17841))
Explore B9WJ66 
Go to UniProtKB:  B9WJ66
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB9WJ66
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.46 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.97α = 90
b = 64.55β = 91.07
c = 96.05γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-07-01
    Changes: Database references