5YFE

Enzymatic and structural characterization of the poly (ethylene terephthalate) hydrolase PETase from I. sakaiensis

• PDB DOI: https://doi.org/10.2210/pdb5YFE/pdb

• Classification: HYDROLASE
• Organism(s): Piscinibacter sakaiensis
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-09-21 Released: 2018-09-26 
• Deposition Author(s): Bao, R., He, L.H., Liu, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.235 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 

Literature

Protein Crystallography and Site-Direct Mutagenesis Analysis of the Poly(ethylene terephthalate) Hydrolase PETase from Ideonella sakaiensis.

Liu, B., He, L., Wang, L., Li, T., Li, C., Liu, H., Luo, Y., Bao, R.

(2018) Chembiochem 

• PubMed: 29603535 
• DOI: https://doi.org/10.1002/cbic.201800097
• Primary Citation of Related Structures:  
  5YFE


• PubMed Abstract: 
  

  Unlike traditional recycling strategies, biodegradation is a sustainable solution for disposing of poly(ethylene terephthalate) (PET) waste. PETase, a newly identified enzyme from Ideonella sakaiensis, has high efficiency and specificity towards PET and is, thus, a prominent candidate for PET degradation. On the basis of biochemical analysis, we propose that a wide substrate-binding pocket is critical for its excellent ability to hydrolyze crystallized PET. Structure-guided site-directed mutagenesis revealed an improvement in PETase catalytic efficiency, providing valuable insight into how the molecular engineering of PETase can optimize its application in biocatalysis.

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Organizational Affiliation: 

Department of Gastroenterology, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu, 610041, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 29.07 kDa 
• Atom Count: 2,065 
• Modelled Residue Count: 268 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Poly(ethylene terephthalate) hydrolase	A	272	Piscinibacter sakaiensis	Mutation(s): 3  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	D [auth A], E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 0.235 
• R-Value Work: 0.223 
• R-Value Observed: 0.223 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.945	α = 90
b = 56.644	β = 90
c = 80.611	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Bao, R., He, L.H., Liu, B.

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2019-04-10
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description