8C4Z | pdb_00008c4z

ProteinT protease, inactive mutant S224A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 
    0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work: 
    0.139 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 
    0.141 (Depositor) 

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

Validation slider image for 8C4Z

This is version 1.4 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 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.

Macromolecule Content 

  • Total Structure Weight: 41.34 kDa 
  • Atom Count: 3,382 
  • Modeled Residue Count: 394 
  • Deposited Residue Count: 394 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Extracellular serine proteinase112Thermus sp. Rt41AMutation(s): 0 
EC: 3.4.21
UniProt
Find proteins for P80146 (Thermus sp. (strain Rt41A))
Explore P80146 
Go to UniProtKB:  P80146
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80146
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Extracellular serine proteinase282Thermus sp. Rt41AMutation(s): 1 
EC: 3.4.21
UniProt
Find proteins for P80146 (Thermus sp. (strain Rt41A))
Explore P80146 
Go to UniProtKB:  P80146
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP80146
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free:  0.179 (Depositor), 0.179 (DCC) 
  • R-Value Work:  0.139 (Depositor), 0.140 (DCC) 
  • R-Value Observed: 0.141 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.353α = 90
b = 80.559β = 96.97
c = 49.723γ = 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
  • Version 1.4: 2024-10-23
    Changes: Structure summary