IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v15y2024i1d10.1038_s41467-024-50005-9.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-50005-9
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-50005-9?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Amy E. Hutton & Jake Foster & Rebecca Crawshaw & Florence J. Hardy & Linus O. Johannissen & Thomas M. Lister & Emilie F. Gérard & Zachary Birch-Price & Richard Obexer & Sam Hay & Anthony P. Green, 2024. "A non-canonical nucleophile unlocks a new mechanistic pathway in a designed enzyme," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Meng-Fan Wang & Yun-Hu Deng & Yu-Xuan Hong & Jia-Hui Gu & Yong-Yong Cao & Qi Liu & Pierre Braunstein & Jian-Ping Lang, 2023. "In situ observation of a stepwise [2 + 2] photocycloaddition process using fluorescence spectroscopy," Nature Communications, Nature, vol. 14(1), pages 1-9, December.
    3. Jianjian Huang & Tai-Ping Zhou & Ningning Sun & Huaibin Yu & Xixiang Yu & Rong-Zhen Liao & Weijun Yao & Zhifeng Dai & Guojiao Wu & Fangrui Zhong, 2024. "Accessing ladder-shape azetidine-fused indoline pentacycles through intermolecular regiodivergent aza-Paternò–Büchi reactions," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    4. Zi-Lin Li & Shuxin Pei & Ziying Chen & Teng-Yu Huang & Xu-Dong Wang & Lin Shen & Xuebo Chen & Qi-Qiang Wang & De-Xian Wang & Yu-Fei Ao, 2024. "Machine learning-assisted amidase-catalytic enantioselectivity prediction and rational design of variants for improving enantioselectivity," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    5. Huan Sun & Haiyang Jia & Olivia Kendall & Jovan Dragelj & Vladimir Kubyshkin & Tobias Baumann & Maria-Andrea Mroginski & Petra Schwille & Nediljko Budisa, 2022. "Halogenation of tyrosine perturbs large-scale protein self-organization," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    6. Kaiyuan Wang & Qing Hong & Caixia Zhu & Yuan Xu & Wang Li & Ying Wang & Wenhao Chen & Xiang Gu & Xinghua Chen & Yanfeng Fang & Yanfei Shen & Songqin Liu & Yuanjian Zhang, 2024. "Metal-ligand dual-site single-atom nanozyme mimicking urate oxidase with high substrates specificity," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Jun-Kuan Li & Ge Qu & Xu Li & Yuchen Tian & Chengsen Cui & Fa-Guang Zhang & Wuyuan Zhang & Jun-An Ma & Manfred T. Reetz & Zhoutong Sun, 2022. "Rational enzyme design for enabling biocatalytic Baldwin cyclization and asymmetric synthesis of chiral heterocycles," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    8. Antje Krüger & Andrew M. Watkins & Roger Wellington-Oguri & Jonathan Romano & Camila Kofman & Alysse DeFoe & Yejun Kim & Jeff Anderson-Lee & Eli Fisker & Jill Townley & Anne E. d’Aquino & Rhiju Das & , 2023. "Community science designed ribosomes with beneficial phenotypes," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    9. Hongxia Zhao & Wenlong Ding & Jia Zang & Yang Yang & Chao Liu & Linzhen Hu & Yulin Chen & Guanglong Liu & Yu Fang & Ying Yuan & Shixian Lin, 2021. "Directed-evolution of translation system for efficient unnatural amino acids incorporation and generalizable synthetic auxotroph construction," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    10. Peihua Lin & Bo Zhang & Hongli Yang & Shengfei Yang & Pengpeng Xue & Ying Chen & Shiyi Yu & Jichao Zhang & Yixiao Zhang & Liwei Chen & Chunhai Fan & Fangyuan Li & Daishun Ling, 2024. "An artificial protein modulator reprogramming neuronal protein functions," Nature Communications, Nature, vol. 15(1), pages 1-16, December.
    11. Xudong Wang & Chris Neale & Soo-Kyung Kim & William A. Goddard & Libin Ye, 2023. "Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    12. Enrico Orsi & Lennart Schada von Borzyskowski & Stephan Noack & Pablo I. Nikel & Steffen N. Lindner, 2024. "Automated in vivo enzyme engineering accelerates biocatalyst optimization," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    13. Thuy N. Nguyen & Christine Ingle & Samuel Thompson & Kimberly A. Reynolds, 2024. "The genetic landscape of a metabolic interaction," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    14. Yuda Chen & Shikai Jin & Mengxi Zhang & Yu Hu & Kuan-Lin Wu & Anna Chung & Shichao Wang & Zeru Tian & Yixian Wang & Peter G. Wolynes & Han Xiao, 2022. "Unleashing the potential of noncanonical amino acid biosynthesis to create cells with precision tyrosine sulfation," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    15. Joongoo Lee & Jaime N. Coronado & Namjin Cho & Jongdoo Lim & Brandon M. Hosford & Sangwon Seo & Do Soon Kim & Camila Kofman & Jeffrey S. Moore & Andrew D. Ellington & Eric V. Anslyn & Michael C. Jewet, 2022. "Ribosome-mediated biosynthesis of pyridazinone oligomers in vitro," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    16. Yiman Gao & Jie Liu & Cong Wei & Yan Li & Kui Zhang & Liangliang Song & Lingchao Cai, 2022. "Photoinduced β-fragmentation of aliphatic alcohol derivatives for forging C–C bonds," Nature Communications, Nature, vol. 13(1), pages 1-9, December.
    17. Vaitea Opuu & Giuliano Nigro & Thomas Gaillard & Emmanuelle Schmitt & Yves Mechulam & Thomas Simonson, 2020. "Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power," PLOS Computational Biology, Public Library of Science, vol. 16(1), pages 1-19, January.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-50005-9. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.