Letter | Published:

UbiX is a flavin prenyltransferase required for bacterial ubiquinone biosynthesis

Nature volume 522, pages 502506 (25 June 2015) | Download Citation

Abstract

Ubiquinone (also known as coenzyme Q) is a ubiquitous lipid-soluble redox cofactor that is an essential component of electron transfer chains1. Eleven genes have been implicated in bacterial ubiquinone biosynthesis, including ubiX and ubiD, which are responsible for decarboxylation of the 3-octaprenyl-4-hydroxybenzoate precursor2. Despite structural and biochemical characterization of UbiX as a flavin mononucleotide (FMN)-binding protein, no decarboxylase activity has been detected3,4. Here we report that UbiX produces a novel flavin-derived cofactor required for the decarboxylase activity of UbiD5. UbiX acts as a flavin prenyltransferase, linking a dimethylallyl moiety to the flavin N5 and C6 atoms. This adds a fourth non-aromatic ring to the flavin isoalloxazine group. In contrast to other prenyltransferases6,7, UbiX is metal-independent and requires dimethylallyl-monophosphate as substrate. Kinetic crystallography reveals that the prenyltransferase mechanism of UbiX resembles that of the terpene synthases8. The active site environment is dominated by π systems, which assist phosphate-C1′ bond breakage following FMN reduction, leading to formation of the N5–C1′ bond. UbiX then acts as a chaperone for adduct reorientation, via transient carbocation species, leading ultimately to formation of the dimethylallyl C3′–C6 bond. Our findings establish the mechanism for formation of a new flavin-derived cofactor, extending both flavin and terpenoid biochemical repertoires.

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Accessions

Data deposits

Coordinates and structure factors have been deposited in the Protein Data Bank under accession numbers 4ZAF, 4ZAV, 4ZAW, 4ZAX, 4ZAG, 4ZAL, 4ZAY, 4ZAN and 4ZAZ.

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Acknowledgements

This work was supported by BBSRC grants (BB/K017802/1 with Shell and BB/M017702/1). We thank Diamond Light Source for access to beamlines (proposal number MX8997) that contributed to the results presented here. S.H. is a BBSRC David Phillips research fellow. N.S.S. is an EPSRC Established Career Fellow and Royal Society Wolfson Award holder. The authors acknowledge the assistance given by IT Services and the use of the Computational Shared Facility and the Protein Structure Facility at The University of Manchester.

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Affiliations

  1. Centre for Synthetic Biology of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, UK

    • Mark D. White
    • , Karl A. P. Payne
    • , Karl Fisher
    • , Stephen A. Marshall
    • , Nicholas J. W. Rattray
    • , Drupad K. Trivedi
    • , Royston Goodacre
    • , Stephen E. J. Rigby
    • , Nigel S. Scrutton
    • , Sam Hay
    •  & David Leys
  2. Innovation/Biodomain, Shell International Exploration and Production, Westhollow Technology Center, 3333 Highway 6 South, Houston, Texas 77082-3101, USA

    • David Parker

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Contributions

M.D.W. carried out molecular biology, biophysical and structural biology studies together with K.A.P.P. and D.L. M.D.W. and S.A.M. performed in vitro reconstitution experiments. K.F. and S.E.J.R. performed and analysed EPR experiments. S.H. performed DFT calculations. N.J.W.R. and D.K.T. undertook liquid chromatography–mass spectrometry of extracts and with R.G. interpreted the data on substrate–product species. All authors discussed the results with D.P and N.S.S. and participated in writing the manuscript. D.L. initiated and directed this research.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to David Leys.

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    Supplementary Data 1

    Cartesian coordinates of optimized DFT models.

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https://doi.org/10.1038/nature14559

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