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Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters

Abstract

Biotin is an essential vitamin in plants and mammals, functioning as the carbon dioxide carrier within central lipid metabolism. Bacterial pimeloyl-CoA synthetase (BioW) acts as a highly specific substrate-selection gate, ensuring the integrity of the carbon chain in biotin synthesis. BioW catalyzes the condensation of pimelic acid (C7 dicarboxylic acid) with CoASH in an ATP-dependent manner to form pimeloyl-CoA, the first dedicated biotin building block. Multiple structures of Bacillus subtilis BioW together capture all three substrates, as well as the intermediate pimeloyl-adenylate and product pyrophosphate (PPi), indicating that the enzyme uses an internal ruler to select the correct dicarboxylic acid substrate. Both the catalytic mechanism and the surprising stability of the adenylate intermediate were rationalized through site-directed mutagenesis. Building on this understanding, BioW was engineered to synthesize high-value heptanoyl (C7) and octanoyl (C8) monocarboxylic acid-CoA and C8 dicarboxylic-CoA products, highlighting the enzyme's synthetic potential.

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Figure 1: The BioW reaction, highlighting its role in biotin biosynthesis and the activity of wild-type BioW with various fatty acid substrates.
Figure 2: Structural biology of BioW.
Figure 3: Native MS analysis of BioW.
Figure 4: Activity of wild-type BioW and active site mutants toward pimelic acid and assays to determine the chain-length specificity of BioW and designed mutants.
Figure 5: Synthesis of heptanoyl-CoA by the engineered BioW Y211F mutant.
Figure 6: Schematic of the BioW active site.

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Acknowledgements

This work was supported by grants from the Biotechnology and Biological Sciences Research Council (BBSRC, BB/M003493/1) (D.J.C. and J.H.N.) and Wellcome Trust (WT100209MA (J.H.N.)). The native MS data were acquired on an instrument funded by an Engineering and Physical Sciences Research Council (EPSRC) grant to the University of Edinburgh (EP/K039717/1). We acknowledge the use of the Diamond synchrotron. J.H.N. is a Royal Society Wolfson Merit Award Holder and 1000 talent scholar at Sichuan University. M.W. was funded by a University of Edinburgh PhD scholarship. We thank B. Mykhaylyk for help with bioinformatics analysis and L. Mackay for help with MS analysis.

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Contributions

A.P. carried out the initial cloning of the bioW gene and characterization of the recombinant BioW. M.W. and P.J.H. carried out the enzyme isolation, characterization and assay. M.W. generated all the BioW mutants and determined the kinetic parameters of wild-type and mutant enzymes. V.K. performed all protein and acyl-CoA MS analyses. M.W. and L.M. prepared the enzyme for crystal trials and optimized crystallization conditions. L.M. carried out the crystallography experiments with J.H.N. and acquired and interpreted the data. L.M., M.W., P.J.H., V.K., J.H.N. and D.J.C. interpreted the data and wrote the paper.

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Correspondence to James H Naismith or Dominic J Campopiano.

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The authors declare no competing financial interests.

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Wang, M., Moynié, L., Harrison, P. et al. Using the pimeloyl-CoA synthetase adenylation fold to synthesize fatty acid thioesters. Nat Chem Biol 13, 660–667 (2017). https://doi.org/10.1038/nchembio.2361

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