IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-37415-x.html
   My bibliography  Save this article

Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product

Author

Listed:
  • P. Konstantin Richter

    (Leipzig University)

  • Paula Blázquez-Sánchez

    (Leipzig University)

  • Ziyue Zhao

    (Leipzig University)

  • Felipe Engelberger

    (Leipzig University Medical School)

  • Christian Wiebeler

    (Leipzig University
    Leipzig University)

  • Georg Künze

    (Leipzig University Medical School)

  • Ronny Frank

    (Leipzig University)

  • Dana Krinke

    (Leipzig University)

  • Emanuele Frezzotti

    (University of Parma)

  • Yuliia Lihanova

    (Leipzig University)

  • Patricia Falkenstein

    (Leipzig University)

  • Jörg Matysik

    (Leipzig University)

  • Wolfgang Zimmermann

    (Leipzig University)

  • Norbert Sträter

    (Leipzig University)

  • Christian Sonnendecker

    (Leipzig University)

Abstract

The recently discovered metagenomic-derived polyester hydrolase PHL7 is able to efficiently degrade amorphous polyethylene terephthalate (PET) in post-consumer plastic waste. We present the cocrystal structure of this hydrolase with its hydrolysis product terephthalic acid and elucidate the influence of 17 single mutations on the PET-hydrolytic activity and thermal stability of PHL7. The substrate-binding mode of terephthalic acid is similar to that of the thermophilic polyester hydrolase LCC and deviates from the mesophilic IsPETase. The subsite I modifications L93F and Q95Y, derived from LCC, increased the thermal stability, while exchange of H185S, derived from IsPETase, reduced the stability of PHL7. The subsite II residue H130 is suggested to represent an adaptation for high thermal stability, whereas L210 emerged as the main contributor to the observed high PET-hydrolytic activity. Variant L210T showed significantly higher activity, achieving a degradation rate of 20 µm h−1 with amorphous PET films.

Suggested Citation

  • P. Konstantin Richter & Paula Blázquez-Sánchez & Ziyue Zhao & Felipe Engelberger & Christian Wiebeler & Georg Künze & Ronny Frank & Dana Krinke & Emanuele Frezzotti & Yuliia Lihanova & Patricia Falken, 2023. "Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-37415-x
    DOI: 10.1038/s41467-023-37415-x
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-37415-x
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-37415-x?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. Sarel J Fleishman & Andrew Leaver-Fay & Jacob E Corn & Eva-Maria Strauch & Sagar D Khare & Nobuyasu Koga & Justin Ashworth & Paul Murphy & Florian Richter & Gordon Lemmon & Jens Meiler & David Baker, 2011. "RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite," PLOS ONE, Public Library of Science, vol. 6(6), pages 1-10, June.
    2. Xu Han & Weidong Liu & Jian-Wen Huang & Jiantao Ma & Yingying Zheng & Tzu-Ping Ko & Limin Xu & Ya-Shan Cheng & Chun-Chi Chen & Rey-Ting Guo, 2017. "Structural insight into catalytic mechanism of PET hydrolase," Nature Communications, Nature, vol. 8(1), pages 1-6, December.
    3. Seongjoon Joo & In Jin Cho & Hogyun Seo & Hyeoncheol Francis Son & Hye-Young Sagong & Tae Joo Shin & So Young Choi & Sang Yup Lee & Kyung-Jin Kim, 2018. "Structural insight into molecular mechanism of poly(ethylene terephthalate) degradation," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    4. Hongyuan Lu & Daniel J. Diaz & Natalie J. Czarnecki & Congzhi Zhu & Wantae Kim & Raghav Shroff & Daniel J. Acosta & Bradley R. Alexander & Hannah O. Cole & Yan Zhang & Nathaniel A. Lynd & Andrew D. El, 2022. "Machine learning-aided engineering of hydrolases for PET depolymerization," Nature, Nature, vol. 604(7907), pages 662-667, April.
    5. V. Tournier & C. M. Topham & A. Gilles & B. David & C. Folgoas & E. Moya-Leclair & E. Kamionka & M.-L. Desrousseaux & H. Texier & S. Gavalda & M. Cot & E. Guémard & M. Dalibey & J. Nomme & G. Cioci & , 2020. "An engineered PET depolymerase to break down and recycle plastic bottles," Nature, Nature, vol. 580(7802), pages 216-219, April.
    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. Hwaseok Hong & Dongwoo Ki & Hogyun Seo & Jiyoung Park & Jaewon Jang & Kyung-Jin Kim, 2023. "Discovery and rational engineering of PET hydrolase with both mesophilic and thermophilic PET hydrolase properties," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    2. Zhuozhi Chen & Rongdi Duan & Yunjie Xiao & Yi Wei & Hanxiao Zhang & Xinzhao Sun & Shen Wang & Yingying Cheng & Xue Wang & Shanwei Tong & Yunxiao Yao & Cheng Zhu & Haitao Yang & Yanyan Wang & Zefang Wa, 2022. "Biodegradation of highly crystallized poly(ethylene terephthalate) through cell surface codisplay of bacterial PETase and hydrophobin," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    3. Trishnamoni Gautom & Dharmendra Dheeman & Colin Levy & Thomas Butterfield & Guadalupe Alvarez Gonzalez & Philip Roy & Lewis Caiger & Karl Fisher & Linus Johannissen & Neil Dixon, 2021. "Structural basis of terephthalate recognition by solute binding protein TphC," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Anni Li & Yijie Sheng & Haiyang Cui & Minghui Wang & Luxuan Wu & Yibo Song & Rongrong Yang & Xiujuan Li & He Huang, 2023. "Discovery and mechanism-guided engineering of BHET hydrolases for improved PET recycling and upcycling," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    5. Erika Erickson & Japheth E. Gado & Luisana Avilán & Felicia Bratti & Richard K. Brizendine & Paul A. Cox & Raj Gill & Rosie Graham & Dong-Jin Kim & Gerhard König & William E. Michener & Saroj Poudel &, 2022. "Sourcing thermotolerant poly(ethylene terephthalate) hydrolase scaffolds from natural diversity," Nature Communications, Nature, vol. 13(1), pages 1-15, December.
    6. Teng Bao & Yuanchao Qian & Yongping Xin & James J. Collins & Ting Lu, 2023. "Engineering microbial division of labor for plastic upcycling," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    7. Katarzyna Świderek & Susana Velasco-Lozano & Miquel À. Galmés & Ion Olazabal & Haritz Sardon & Fernando López-Gallego & Vicent Moliner, 2023. "Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    8. Yu Yang & Jian Min & Ting Xue & Pengcheng Jiang & Xin Liu & Rouming Peng & Jian-Wen Huang & Yingying Qu & Xian Li & Ning Ma & Fang-Chang Tsai & Longhai Dai & Qi Zhang & Yingle Liu & Chun-Chi Chen & Re, 2023. "Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases," Nature Communications, Nature, vol. 14(1), pages 1-8, December.
    9. Yinglu Cui & Yanchun Chen & Jinyuan Sun & Tong Zhu & Hua Pang & Chunli Li & Wen-Chao Geng & Bian Wu, 2024. "Computational redesign of a hydrolase for nearly complete PET depolymerization at industrially relevant high-solids loading," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    10. Huang, Jijiang & Veksha, Andrei & Chan, Wei Ping & Giannis, Apostolos & Lisak, Grzegorz, 2022. "Chemical recycling of plastic waste for sustainable material management: A prospective review on catalysts and processes," Renewable and Sustainable Energy Reviews, Elsevier, vol. 154(C).
    11. Daniel Ellis & Julia Lederhofer & Oliver J. Acton & Yaroslav Tsybovsky & Sally Kephart & Christina Yap & Rebecca A. Gillespie & Adrian Creanga & Audrey Olshefsky & Tyler Stephens & Deleah Pettie & Mic, 2022. "Structure-based design of stabilized recombinant influenza neuraminidase tetramers," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    12. Yuantao Peng & Jie Yang & Chenqiang Deng & Jin Deng & Li Shen & Yao Fu, 2023. "Acetolysis of waste polyethylene terephthalate for upcycling and life-cycle assessment study," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    13. Jonathan Yaacov Weinstein & Carlos Martí-Gómez & Rosalie Lipsh-Sokolik & Shlomo Yakir Hoch & Demian Liebermann & Reinat Nevo & Haim Weissman & Ekaterina Petrovich-Kopitman & David Margulies & Dmitry I, 2023. "Designed active-site library reveals thousands of functional GFP variants," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    14. Jared Adolf-Bryfogle & Oleks Kalyuzhniy & Michael Kubitz & Brian D Weitzner & Xiaozhen Hu & Yumiko Adachi & William R Schief & Roland L Dunbrack Jr., 2018. "RosettaAntibodyDesign (RAbD): A general framework for computational antibody design," PLOS Computational Biology, Public Library of Science, vol. 14(4), pages 1-38, April.
    15. Xinlei Wei & Xue Yang & Congcong Hu & Qiangzi Li & Qianqian Liu & Yue Wu & Leipeng Xie & Xiao Ning & Fei Li & Tao Cai & Zhiguang Zhu & Yi-Heng P. Job Zhang & Yanfei Zhang & Xuejun Chen & Chun You, 2024. "ATP-free in vitro biotransformation of starch-derived maltodextrin into poly-3-hydroxybutyrate via acetyl-CoA," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    16. Vishruth Mullapudi & Jaime Vaquer-Alicea & Vaibhav Bommareddy & Anthony R. Vega & Bryan D. Ryder & Charles L. White & Marc. I. Diamond & Lukasz A. Joachimiak, 2023. "Network of hotspot interactions cluster tau amyloid folds," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    17. Jun Qi & Yadong Du & Qi Yang & Na Jiang & Jiachun Li & Yi Ma & Yangjun Ma & Xin Zhao & Jieshan Qiu, 2023. "Energy-saving and product-oriented hydrogen peroxide electrosynthesis enabled by electrochemistry pairing and product engineering," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    18. Elizabeth L. Bell & Gloria Rosetto & Morgan A. Ingraham & Kelsey J. Ramirez & Clarissa Lincoln & Ryan W. Clarke & Japheth E. Gado & Jacob L. Lilly & Katarzyna H. Kucharzyk & Erika Erickson & Gregg T. , 2024. "Natural diversity screening, assay development, and characterization of nylon-6 enzymatic depolymerization," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    19. Gluth, A. & Xu, Z. & Fifield, L.S. & Yang, B., 2022. "Advancing biological processing for valorization of plastic wastes," Renewable and Sustainable Energy Reviews, Elsevier, vol. 170(C).
    20. Kamali, Ali Reza & Li, Siyuan, 2023. "Molten salt-assisted valorization of waste PET plastics into nanostructured SnO2@terephthalic acid with excellent Li-ion storage performance," Applied Energy, Elsevier, vol. 334(C).

    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:14:y:2023:i:1:d:10.1038_s41467-023-37415-x. 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.