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Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase

Abstract

Aromatic prenyltransferases (aPTases) transfer prenyl moieties from isoprenoid donors to various aromatic acceptors, some of which have the rare property of extreme enzymatic promiscuity toward both a variety of prenyl donors and a large diversity of acceptors. In this study, we discovered a new aPTase, AtaPT, from Aspergillus terreus that exhibits unprecedented promiscuity toward diverse aromatic acceptors and prenyl donors and also yields products with a range of prenylation patterns. Systematic crystallographic studies revealed various discrete conformations for ligand binding with donor-dependent acceptor specificity and multiple binding sites within a spacious hydrophobic substrate-binding pocket. Further structure-guided mutagenesis of active sites at the substrate-binding pocket is responsible for altering the specificity and promiscuity toward substrates and the diversity of product prenylations. Our study reveals the molecular mechanism underlying the promiscuity of AtaPT and suggests an efficient protein engineering strategy to generate new prenylated derivatives in drug discovery applications.

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Figure 1: Structures of the aromatic compounds assayed as prenyl acceptors.
Figure 2: Prenylation of aromatics by AtaPT.
Figure 3: Crystal structure of AtaPT and its catalytic chamber.
Figure 4: Donor-dependent acceptor binding by AtaPT.
Figure 5: Conformational dynamics of the tyrosine shield and various acceptor binding sites of AtaPT.
Figure 6: Structure-guided mutagenesis of AtaPT to alter its substrate promiscuity.

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Acknowledgements

We thank S. Huang and J. He for their on-site assistance with the crystallographic data collection at the SSRF beamline BL17U. This work was supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB08030202) to F.S., the National Basic Research Program (973 Program) of Ministry of Science and Technology of China (2014CB910700) to F.S. and (2014CB910202) to J.L., the National Natural Science Foundation of China (81302667) to R.C. and the Deutsche Forschungsgemeinschaft (Li844/4-1) to S.-M.L. The computational resources were provided by the National Supercomputing Center in Tianjin and the HPC-Service Station at the Center for Biological Imaging of the Institute of Biophysics of the Chinese Academy of Sciences.

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J.D., S.-M.L. and F.S. supervised the project. R.C., X.L., F.R., C.W. and K.F. performed the enzymatic and chemical experiments. B.G. performed the crystallographic and ITC experiments. Y.Z. and J.L. performed the molecular dynamics simulations. R.C., X.L., B.G., J.D. and F.S. analyzed the data and wrote the manuscript.

Corresponding authors

Correspondence to Jungui Dai or Fei Sun.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1–6 and Supplementary Figures 1–17. (PDF 2879 kb)

Supplementary Note

The spectroscopic data of identified catalytic products by AtaPT and the corresponding spectra. (PDF 10265 kb)

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Chen, R., Gao, B., Liu, X. et al. Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase. Nat Chem Biol 13, 226–234 (2017). https://doi.org/10.1038/nchembio.2263

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