6EQE

High resolution crystal structure of a polyethylene terephthalate degrading hydrolase from Ideonella sakaiensis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.110 
  • R-Value Work: 0.100 
  • R-Value Observed: 0.101 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Characterization and engineering of a plastic-degrading aromatic polyesterase.

Austin, H.P.Allen, M.D.Donohoe, B.S.Rorrer, N.A.Kearns, F.L.Silveira, R.L.Pollard, B.C.Dominick, G.Duman, R.El Omari, K.Mykhaylyk, V.Wagner, A.Michener, W.E.Amore, A.Skaf, M.S.Crowley, M.F.Thorne, A.W.Johnson, C.W.Woodcock, H.L.McGeehan, J.E.Beckham, G.T.

(2018) Proc Natl Acad Sci U S A 115: E4350-E4357

  • DOI: 10.1073/pnas.1718804115
  • Primary Citation of Related Structures:  
    6EQE, 6EQD, 6EQG, 6EQF, 6EQH

  • PubMed Abstract: 
  • Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an ...

    Poly(ethylene terephthalate) (PET) is one of the most abundantly produced synthetic polymers and is accumulating in the environment at a staggering rate as discarded packaging and textiles. The properties that make PET so useful also endow it with an alarming resistance to biodegradation, likely lasting centuries in the environment. Our collective reliance on PET and other plastics means that this buildup will continue unless solutions are found. Recently, a newly discovered bacterium, Ideonella sakaiensis 201-F6, was shown to exhibit the rare ability to grow on PET as a major carbon and energy source. Central to its PET biodegradation capability is a secreted PETase (PET-digesting enzyme). Here, we present a 0.92 Å resolution X-ray crystal structure of PETase, which reveals features common to both cutinases and lipases. PETase retains the ancestral α/β-hydrolase fold but exhibits a more open active-site cleft than homologous cutinases. By narrowing the binding cleft via mutation of two active-site residues to conserved amino acids in cutinases, we surprisingly observe improved PET degradation, suggesting that PETase is not fully optimized for crystalline PET degradation, despite presumably evolving in a PET-rich environment. Additionally, we show that PETase degrades another semiaromatic polyester, polyethylene-2,5-furandicarboxylate (PEF), which is an emerging, bioderived PET replacement with improved barrier properties. In contrast, PETase does not degrade aliphatic polyesters, suggesting that it is generally an aromatic polyesterase. These findings suggest that additional protein engineering to increase PETase performance is realistic and highlight the need for further developments of structure/activity relationships for biodegradation of synthetic polyesters.


    Organizational Affiliation

    National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401; hlw@mail.usf.edu john.mcgeehan@port.ac.uk gregg.beckham@nrel.gov.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(ethylene terephthalate) hydrolaseA298Ideonella sakaiensisMutation(s): 0 
Gene Names: ISF6_4831
EC: 3.1.1.101
Find proteins for A0A0K8P6T7 (Ideonella sakaiensis (strain NBRC 110686 / TISTR 2288 / 201-F6))
Explore A0A0K8P6T7 
Go to UniProtKB:  A0A0K8P6T7
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.92 Å
  • R-Value Free: 0.110 
  • R-Value Work: 0.100 
  • R-Value Observed: 0.101 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.114α = 90
b = 51.388β = 90
c = 84.545γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
NRELUnited StatesLaboratory Directed Research and Development Program
Biotechnology and Biological Sciences Research CouncilUnited KingdomBB/P011918/1

Revision History 

  • Version 1.0: 2018-04-25
    Type: Initial release
  • Version 1.1: 2018-05-02
    Changes: Data collection, Database references
  • Version 1.2: 2018-05-16
    Changes: Data collection, Database references