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Genetically encoded Nδ-vinyl histidine for the evolution of enzyme catalytic center

Author

Listed:
  • Haoran Huang

    (Southern University of Science and Technology)

  • Tao Yan

    (Southern University of Science and Technology)

  • Chang Liu

    (Southern University of Science and Technology)

  • Yuxiang Lu

    (Southern University of Science and Technology)

  • Zhigang Wu

    (Southern University of Science and Technology)

  • Xingchu Wang

    (Southern University of Science and Technology)

  • Jie Wang

    (Southern University of Science and Technology)

Abstract

Genetic code expansion has emerged as a powerful tool for precisely introducing unnatural chemical structures into proteins to improve their catalytic functions. Given the high catalytic propensity of histidine in the enzyme pocket, increasing the chemical diversity of catalytic histidine could result in new characteristics of biocatalysts. Herein, we report the genetically encoded Nδ-Vinyl Histidine (δVin-H) and achieve the wild-type-like incorporation efficiency by the evolution of pyrrolysyl tRNA synthetase. As histidine usually acts as the nucleophile or the metal ligand in the catalytic center, we replace these two types of catalytic histidine to δVin-H to improve the performance of the histidine-involved catalytic center. Additionally, we further demonstrate the improvements of the hydrolysis activity of a previously reported organocatalytic esterase (the OE1.3 variant) in the acidic condition and myoglobin (Mb) catalyzed carbene transfer reactions under the aerobic condition. As histidine is one of the most frequently used residues in the enzyme catalytic center, the derivatization of the catalytic histidine by δVin-H holds a great potential to promote the performance of biocatalysts.

Suggested Citation

  • Haoran Huang & Tao Yan & Chang Liu & Yuxiang Lu & Zhigang Wu & Xingchu Wang & Jie Wang, 2024. "Genetically encoded Nδ-vinyl histidine for the evolution of enzyme catalytic center," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50005-9
    DOI: 10.1038/s41467-024-50005-9
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    References listed on IDEAS

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    1. Jason W. Chin, 2017. "Expanding and reprogramming the genetic code," Nature, Nature, vol. 550(7674), pages 53-60, October.
    2. Ashleigh J. Burke & Sarah L. Lovelock & Amina Frese & Rebecca Crawshaw & Mary Ortmayer & Mark Dunstan & Colin Levy & Anthony P. Green, 2019. "Design and evolution of an enzyme with a non-canonical organocatalytic mechanism," Nature, Nature, vol. 570(7760), pages 219-223, June.
    3. Sarah L. Lovelock & Rebecca Crawshaw & Sophie Basler & Colin Levy & David Baker & Donald Hilvert & Anthony P. Green, 2022. "The road to fully programmable protein catalysis," Nature, Nature, vol. 606(7912), pages 49-58, June.
    4. Jonathan S. Trimble & Rebecca Crawshaw & Florence J. Hardy & Colin W. Levy & Murray J. B. Brown & Douglas E. Fuerst & Derren J. Heyes & Richard Obexer & Anthony P. Green, 2022. "A designed photoenzyme for enantioselective [2+2] cycloadditions," Nature, Nature, vol. 611(7937), pages 709-714, November.
    5. Ningning Sun & Jianjian Huang & Junyi Qian & Tai-Ping Zhou & Juan Guo & Langyu Tang & Wentao Zhang & Yaming Deng & Weining Zhao & Guojiao Wu & Rong-Zhen Liao & Xi Chen & Fangrui Zhong & Yuzhou Wu, 2022. "Enantioselective [2+2]-cycloadditions with triplet photoenzymes," Nature, Nature, vol. 611(7937), pages 715-720, November.
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