8C4X

PAM Protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

An engineered enzyme embedded into PLA to make self-biodegradable plastic.

Guicherd, M.Ben Khaled, M.Gueroult, M.Nomme, J.Dalibey, M.Grimaud, F.Alvarez, P.Kamionka, E.Gavalda, S.Noel, M.Vuillemin, M.Amillastre, E.Labourdette, D.Cioci, G.Tournier, V.Kitpreechavanich, V.Dubois, P.Andre, I.Duquesne, S.Marty, A.

(2024) Nature 631: 884-890

  • DOI: https://doi.org/10.1038/s41586-024-07709-1
  • Primary Citation of Related Structures:  
    8C4X, 8C4Z

  • PubMed Abstract: 

    Plastic production reached 400 million tons in 2022 (ref. 1 ), with packaging and single-use plastics accounting for a substantial amount of this 2 . The resulting waste ends up in landfills, incineration or the environment, contributing to environmental pollution 3 . Shifting to biodegradable and compostable plastics is increasingly being considered as an efficient waste-management alternative 4 . Although polylactide (PLA) is the most widely used biosourced polymer 5 , its biodegradation rate under home-compost and soil conditions remains low 6-8 . Here we present a PLA-based plastic in which an optimized enzyme is embedded to ensure rapid biodegradation and compostability at room temperature, using a scalable industrial process. First, an 80-fold activity enhancement was achieved through structure-based rational engineering of a new hyperthermostable PLA hydrolase. Second, the enzyme was uniformly dispersed within the PLA matrix by means of a masterbatch-based melt extrusion process. The liquid enzyme formulation was incorporated in polycaprolactone, a low-melting-temperature polymer, through melt extrusion at 70 °C, forming an 'enzymated' polycaprolactone masterbatch. Masterbatch pellets were integrated into PLA by melt extrusion at 160 °C, producing an enzymated PLA film (0.02% w/w enzyme) that fully disintegrated under home-compost conditions within 20-24 weeks, meeting home-composting standards. The mechanical and degradation properties of the enzymated film were compatible with industrial packaging applications, and they remained intact during long-term storage. This innovative material not only opens new avenues for composters and biomethane production but also provides a feasible industrial solution for PLA degradation.


  • Organizational Affiliation

    Toulouse Biotechnology Institute, Université de Toulouse, CNRS, INRAE, INSA, Toulouse, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protease276Actinomadura keratinilyticaMutation(s): 0 
Gene Names: prt
UniProt
Find proteins for A0A0U5AS91 (Actinomadura sp. RD001933)
Explore A0A0U5AS91 
Go to UniProtKB:  A0A0U5AS91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U5AS91
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protease81Actinomadura keratinilyticaMutation(s): 0 
Gene Names: prt
UniProt
Find proteins for A0A0U5AS91 (Actinomadura sp. RD001933)
Explore A0A0U5AS91 
Go to UniProtKB:  A0A0U5AS91
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0U5AS91
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TRS
Query on TRS

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MPD
Query on MPD

Download Ideal Coordinates CCD File 
C [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
F [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.150 
  • R-Value Observed: 0.151 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.482α = 90
b = 64.175β = 96.16
c = 62.959γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Institute of Agricultural Research (INRAE)France--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-17
    Type: Initial release
  • Version 1.1: 2024-07-24
    Changes: Database references
  • Version 1.2: 2024-07-31
    Changes: Database references
  • Version 1.3: 2024-08-07
    Changes: Database references