7XTW | pdb_00007xtw

The structure of IsPETase in complex with MHET


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.149 (Depositor), 0.150 (DCC) 
  • R-Value Work: 
    0.136 (Depositor), 0.136 (DCC) 
  • R-Value Observed: 
    0.137 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Complete bio-degradation of poly(butylene adipate-co-terephthalate) via engineered cutinases.

Yang, Y.Min, J.Xue, T.Jiang, P.Liu, X.Peng, R.Huang, J.W.Qu, Y.Li, X.Ma, N.Tsai, F.C.Dai, L.Zhang, Q.Liu, Y.Chen, C.C.Guo, R.T.

(2023) Nat Commun 14: 1645-1645

  • DOI: https://doi.org/10.1038/s41467-023-37374-3
  • Primary Citation Related Structures: 
    7XTR, 7XTS, 7XTT, 7XTU, 7XTV, 7XTW

  • PubMed Abstract: 

    Poly(butylene adipate-co-terephthalate) (PBAT), a polyester made of terephthalic acid (TPA), 1,4-butanediol, and adipic acid, is extensively utilized in plastic production and has accumulated globally as environmental waste. Biodegradation is an attractive strategy to manage PBAT, but an effective PBAT-degrading enzyme is required. Here, we demonstrate that cutinases are highly potent enzymes that can completely decompose PBAT films in 48 h. We further show that the engineered cutinases, by applying a double mutation strategy to render a more flexible substrate-binding pocket exhibit higher decomposition rates. Notably, these variants produce TPA as a major end-product, which is beneficial feature for the future recycling economy. The crystal structures of wild type and double mutation of a cutinase from Thermobifida fusca in complex with a substrate analogue are also solved, elucidating their substrate-binding modes. These structural and biochemical analyses enable us to propose the mechanism of cutinase-mediated PBAT degradation.


  • Organizational Affiliation
    • State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Hongshan Laboratory, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, 430062, Wuhan, People's Republic of China.

Macromolecule Content 

  • Total Structure Weight: 28.36 kDa 
  • Atom Count: 2,235 
  • Modeled Residue Count: 261 
  • Deposited Residue Count: 262 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Poly(ethylene terephthalate) hydrolase262Piscinibacter sakaiensisMutation(s): 2 
Gene Names: ISF6_4831
EC: 3.1.1.101
UniProt
Find proteins for A0A0K8P6T7 (Piscinibacter sakaiensis)
Explore A0A0K8P6T7 
Go to UniProtKB:  A0A0K8P6T7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K8P6T7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C9C
(Subject of Investigation/LOI)

Query on C9C



Download:Ideal Coordinates CCD File
C [auth A]4-(2-hydroxyethyloxycarbonyl)benzoic acid
C10 H10 O5
BCBHDSLDGBIFIX-UHFFFAOYSA-N
TRS

Query on TRS



Download:Ideal Coordinates CCD File
J [auth A]2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A],
E [auth A],
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
B [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.149 (Depositor), 0.150 (DCC) 
  • R-Value Work:  0.136 (Depositor), 0.136 (DCC) 
  • R-Value Observed: 0.137 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.836α = 90
b = 50.889β = 90
c = 84.097γ = 90
Software Package:
Software NamePurpose
SADABSdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
SAINTdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China31870790
National Natural Science Foundation of China (NSFC)China31971205
National Natural Science Foundation of China (NSFC)China32101016

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-29
    Type: Initial release
  • Version 1.1: 2023-04-12
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-10-16
    Changes: Structure summary