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Abstract

Introduction of innovative biocatalytic processes offers great promise for applications in green chemistry. However, owing to limited catalytic performance, the enzymes harvested from nature's biodiversity often need to be improved for their desired functions by time-consuming iterative rounds of laboratory evolution. Here we describe the use of structure-based computational enzyme design to convert Bacillus sp. YM55-1 aspartase, an enzyme with a very narrow substrate scope, to a set of complementary hydroamination biocatalysts. The redesigned enzymes catalyze asymmetric addition of ammonia to substituted acrylates, affording enantiopure aliphatic, polar and aromatic β-amino acids that are valuable building blocks for the synthesis of pharmaceuticals and bioactive compounds. Without a requirement for further optimization by laboratory evolution, the redesigned enzymes exhibit substrate tolerance up to a concentration of 300 g/L, conversion up to 99%, β-regioselectivity >99% and product enantiomeric excess >99%. The results highlight the use of computational design to rapidly adapt an enzyme to industrially viable reactions.

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Acknowledgements

We thank W. Szymanski for discussions. We thank for the 100 Talent Program grant (B.W.) and Biological Resources Service Network Initiative (ZSYS-012; B.W.) and a grant (SKT1604; C.Y.L.) from the Chinese Academy of Sciences, Natural Science Foundation of China grants (31601412 (B.W.), 21603013 (C.Y.L.)), and a BE-Basic grant (H.J.W. and D.B.J.) from the Dutch Ministry of Economic Affairs for the financial support.

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Author notes

  1. These authors contributed equally: Ruifeng Li, Hein J., Lu Song.

Affiliations

  1. CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China

    • Ruifeng Li
    • , Lu Song
    • , Yinglu Cui
    • , Yu’e Tian
    • , Jiawei Du
    • , Tao Li
    • , Dingding Niu
    • , Yanchun Chen
    • , Jing Feng
    • , Jian Han
    • , Hao Chen
    • , Yong Tao
    •  & Bian Wu
  2. State Key Laboratory of Transducer Technology, Chinese Academy of Sciences, Beijing, China

    • Ruifeng Li
    •  & Yinglu Cui
  3. University of Chinese Academy of Sciences, Beijing, China

    • Ruifeng Li
    • , Jiawei Du
    • , Tao Li
    • , Yanchun Chen
    •  & Jing Feng
  4. Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands

    • Hein J. Wijma
    • , Marleen Otzen
    •  & Dick B. Janssen

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Contributions

D.B.J. and B.W. initiated the project. B.W., H.J.W. and Y. Cui performed the computational work. L.S., R.L., M.O., Y. Tian, J.D., T.L., D.N., Y. Chen and J.F. performed biocatalytic experiments. J.H., H.C. and Y. Tao developed high-density fermentation methods. R.L. performed preparative-scale synthesis of the amino acids. D.B.J. and B.W. provided supervision and input on experimental design and wrote the manuscript, which was revised and approved by all authors. R.L., H.J.W. and L.S. contributed equally to this work.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Dick B. Janssen or Bian Wu.

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DOI

https://doi.org/10.1038/s41589-018-0053-0

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