7SH6

Crystal structure of a PET hydrolase mutant from Ideonella Sakaiensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Machine learning-aided engineering of hydrolases for PET depolymerization.

Lu, H.Diaz, D.J.Czarnecki, N.J.Zhu, C.Kim, W.Shroff, R.Acosta, D.J.Alexander, B.R.Cole, H.O.Zhang, Y.Lynd, N.A.Ellington, A.D.Alper, H.S.

(2022) Nature 604: 662-667

  • DOI: https://doi.org/10.1038/s41586-022-04599-z
  • Primary Citation of Related Structures:  
    7SH6

  • PubMed Abstract: 

    Plastic waste poses an ecological challenge 1-3 and enzymatic degradation offers one, potentially green and scalable, route for polyesters waste recycling 4 . Poly(ethylene terephthalate) (PET) accounts for 12% of global solid waste 5 , and a circular carbon economy for PET is theoretically attainable through rapid enzymatic depolymerization followed by repolymerization or conversion/valorization into other products 6-10 . Application of PET hydrolases, however, has been hampered by their lack of robustness to pH and temperature ranges, slow reaction rates and inability to directly use untreated postconsumer plastics 11 . Here, we use a structure-based, machine learning algorithm to engineer a robust and active PET hydrolase. Our mutant and scaffold combination (FAST-PETase: functional, active, stable and tolerant PETase) contains five mutations compared to wild-type PETase (N233K/R224Q/S121E from prediction and D186H/R280A from scaffold) and shows superior PET-hydrolytic activity relative to both wild-type and engineered alternatives 12 between 30 and 50 °C and a range of pH levels. We demonstrate that untreated, postconsumer-PET from 51 different thermoformed products can all be almost completely degraded by FAST-PETase in 1 week. FAST-PETase can also depolymerize untreated, amorphous portions of a commercial water bottle and an entire thermally pretreated water bottle at 50 ºC. Finally, we demonstrate a closed-loop PET recycling process by using FAST-PETase and resynthesizing PET from the recovered monomers. Collectively, our results demonstrate a viable route for enzymatic plastic recycling at the industrial scale.


  • Organizational Affiliation

    McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Poly(ethylene terephthalate) hydrolase292Piscinibacter sakaiensisMutation(s): 5 
Gene Names: ISF6_4831
EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6))
Explore A0A0K8P6T7 
Go to UniProtKB:  A0A0K8P6T7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K8P6T7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
B [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.44 Å
  • R-Value Free: 0.168 
  • R-Value Work: 0.158 
  • R-Value Observed: 0.158 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.942α = 90
b = 51.182β = 90
c = 84.047γ = 90
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM104896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM125882

Revision History  (Full details and data files)

  • Version 1.0: 2022-04-06
    Type: Initial release
  • Version 1.1: 2022-05-11
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description