Structural insight and engineering of a plastic degrading hydrolase Ple629

Li, Zhishuai; Zhao, Yipei; Wu, Pan; Wang, Hao; Li, Qian; Qin, Hao; Wei, Hongli; Bornscheuer, Uwe T.; Han, Xu; Wei, Ren; Liu, Weidong

doi:10.1016/j.bbrc.2022.07.103

Cited by 17 publications

(8 citation statements)

References 46 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…To date, there is some crystallographic data on the substrate interaction of PET degrading enzymes, however they rely on shorter substrate analogues instead of the PET polymer. 16 , 55 , 56 , 57 In order to circumvent this limitation, MD simulations can be employed, as done here. The value and significance of this method has been demonstrated by several studies that successfully generated improved variants of PET degrading enzymes using MD simulations.…”

Section: Resultsmentioning

confidence: 99%

See 1 more Smart Citation

Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes

et al. 2022

View full text Add to dashboard Cite

The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three‐fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes

et al. 2022

View full text Add to dashboard Cite

show abstract

“…14,30 Computational methods offer insights into the importance of specific residues in the binding site, which complements the limited high-resolution crystal structures of PET hydrolase with small ligands reported recently. 9,14,23,[31][32][33][34][35] Based on the analysis of these structural complexes, it was hypothesized that widening the binding cleft would increase the accessibility of the active site and consequently the enzyme's activity, [36][37][38][39] while narrowing the binding site could enable specific interactions with PET that promote substrate binding and enzyme activity. 40 Since PET is an aromatic, mostly hydrophobic polymer that can form hydrogen bonds, it has been shown that the introduction of aromatic, hydrophobic or hydrogen bond-forming residues also has a positive effect on the efficiency of PET hydrolases.…”

Section: Introductionmentioning

confidence: 99%

From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets

Jäckering,

Göttsch,

Schäffler

et al. 2024

Preprint

Self Cite

View full text Add to dashboard Cite

Plastic-degrading enzymes hold promise for biocatalytic recycling of poly(ethylene terephthalate) (PET), a key synthetic polymer. Despite their potential, the current activity of PET hydrolases is not sufficient for industrial use. To unlock their full potential, a deep mechanistic understanding followed by protein engineering is required. Using cutting-edge molecular dynamics simulations and free energy analysis methods, we uncover the entire pathway from the initial binding of two PET hydrolases - the thermophilic leaf-branch compost cutinase (LCC) and polyester hydrolase 1 (PES-H1) - to an amorphous PET material to a PET chain entering the active site and adopting a hydrolyzable geometry. Our results reveal the initial PET binding and elucidate its non specific nature driven by electrostatic and hydrophobic forces. Upon PET entry into the active site, we uncover that this process can occur via one of three key pathways and detect barriers to it arising from both PET-PET and PET-enzyme interactions, with specific residues identified by in silico and in vitro mutagenesis. These insights not only advance our understanding of PET degradation mechanisms and pave the way for targeted enzyme enhancement strategies, but also offer an innovative approach applicable to enzyme studies across disciplines.

show abstract

“…In 2016, IsPETase and IsMHETase from Ideonella sakaiensis 201-F6 were found to act synergistically to hydrolyze PET to TPA under mesophilic conditions ( Yoshida et al, 2016 ; Palm et al, 2019 ). PBAT shares some structural similarities with PET, and some enzymes have both PET and PBAT hydrolytic activities such as Ples from the marine microbial consortium I1 ( Li et al, 2022 ; Meyer Cifuentes et al, 2022 ) and TfCut from Thermobifida fusca ( Chen et al, 2008 ; Roth et al, 2014 ; Yang et al, 2023 ). Some other enzymes have only been reported to have PBAT hydrolytic activity, such as PpEst from Pseudomonas pseudoalcaligenes was reported to degrade PBAT to terephthalatebutanediol monoester (BT) ( Wallace et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Characterization and engineering of plastic-degrading polyesterases jmPE13 and jmPE14 from Pseudomonas bacterium

Zhou,

et al. 2024

Front. Bioeng. Biotechnol.

View full text Add to dashboard Cite

Polyester plastics are widely used in daily life, but also cause a large amount of waste. Degradation by microbial enzymes is the most promising way for the biobased upcycling of the wastes. However, there is still a shortage of high-performance enzymes, and more efficient polyester hydrolases need to be developed. Here we identified two polyester hydrolases, jmPE13 and jmPE14, from a previously isolated strain Pseudomonas sp. JM16B3. The proteins were recombinantly expressed and purified in E. coli, and their enzymatic properties were characterized. JmPE13 and jmPE14 showed hydrolytic activity towards polyethylene terephthalate (PET) and Poly (butylene adipate-co-terephthalate) (PBAT) at medium temperatures. The enzyme activity and stability of jmPE13 were further improved to 3- and 1.5-fold, respectively, by rational design. The results of our research can be helpful for further engineering of more efficient polyester plastic hydrolases and their industrial applications.

show abstract

Structural insight and engineering of a plastic degrading hydrolase Ple629

Cited by 17 publications

References 46 publications

Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes

Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes

From Bulk to Binding: Decoding the Entry of PET into Hydrolase Binding Pockets

Characterization and engineering of plastic-degrading polyesterases jmPE13 and jmPE14 from Pseudomonas bacterium

Contact Info

Product

Resources

About