ArticleCommunications chemistry2024
The reaction mechanism of the Ideonella sakaiensis PETase enzyme.
Article in Communications chemistry, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
32 citing papers in PubMed, 74 citations in OpenAlex.
- Structural analysis of Sphingobium yanoikuyae P4 carboxylesterase reveals conformational and catalytic determinants for PET biodegradation.World journal of microbiology & biotechnology · 2026Article
- Isosteric Engineering of Enzymes: Overcoming Activity-Stability Trade-Offs by Site-Selective CH → N Substitutions.Angewandte Chemie (International ed. in English) · 2026Article
- Bridging the accuracy-speed divide in reactive molecular dynamics with QuantaMind MD.Science advances · 2026Article
- Molecular bioindicators for assessing environmental impacts of emerging contaminants.Fundamental research · 2026Review
- Application of the YebF secretion pathway inRSC chemical biology · 2026Article
- The aquatic plastisphere: ecology, pathogen dissemination and antimicrobial resistance.Nature reviews. Microbiology · 2026Review
- Challenges and opportunities in the enzymatic recycling of nylons.Nature chemical biology · 2026Review
- Article
- Chitosan nanoparticles as adjuvants to enhance the biodegradation of PET by Ideonella sakaiensis.Applied microbiology and biotechnology · 2026Article
- Inactivation of PETase at Interfaces Inhibits PET Plastic Depolymerization.ACS sustainable chemistry & engineering · 2026Article
- Why Do PETases Struggle with Crystalline PET? Catalytic Ensemble Sampling Reveals Molecular Bottlenecks.The journal of physical chemistry letters · 2026Article
- Catalytic Triad-Inspired Nanozyme Catalysts for Ester Hydrolysis in Organic Solvent Mixtures.ACS catalysis · 2026Article
- Transcriptome data sets ofMicrobiology resource announcements · 2026Article
- Rethinking plastic waste: innovations in enzymatic breakdown of oil-based polyesters and bioplastics.FEBS open bio · 2026Review
- Molecular dynamics simulations of temperature-dependent PET binding in PETase, ThermoPETase, and FAST-PETase.RSC advances · 2026Article
- Temperature-Dependent Active-Site Rearrangements of PETaseSM14: Insights from Molecular Dynamics Simulations.International journal of molecular sciences · 2026Article
- Mechanism of Polyester Hydrolysis by Marine Bacterium PE-H Enzyme: an Atomistic and Thermodynamic Characterization.Journal of chemical information and modeling · 2026Article
- EngineeringiScience · 2026Article
- The effect of ionic strength on PETase enzymes: An experimental and computational study.Protein science : a publication of the Protein Society · 2026Article
- Metagenomic insights into potential PET hydrolases from Antarctic soils and rhizospheres.Frontiers in microbiology · 2026Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
Abstract
Polyethylene terephthalate (PET), the most abundantly produced polyester plastic, can be depolymerized by the Ideonella sakaiensis PETase enzyme. Based on multiple PETase crystal structures, the reaction has been proposed to proceed via a two-step serine hydrolase mechanism mediated by a serine-histidine-aspartate catalytic triad. To elucidate the multi-step PETase catalytic mechanism, we use transition path sampling and likelihood maximization to identify optimal reaction coordinates for the PETase enzyme. We predict that deacylation is likely rate-limiting, and the reaction coordinates for both steps include elements describing nucleophilic attack, ester bond cleavage, and the "moving-histidine" mechanism. We find that the flexibility of Trp185 promotes the reaction, providing an explanation for decreased activity observed in mutations that restrict Trp185 motion. Overall, this study uses unbiased computational approaches to reveal the detailed reaction mechanism necessary for further engineering of an important class of enzymes for plastics bioconversion.
Identifiers
What Socratic holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.