9QV8 | pdb_00009qv8

Polyester Hydrolase Leipzig 7 (PHL7) variant R2M2-A186S


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 
    0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work: 
    0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 
    0.193 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QV8

This is version 1.0 of the entry. See complete history

Literature

Computational engineering of the polyester hydrolase PHL7 for efficient poly(ethylene terephthalate) degradation in biocatalytic recycling processes.

Blazquez-Sanchez, P.Gunkel, J.Useini, A.Zlobin, A.Zakary, J.D.Scholer, A.Graefe, N.Engelberger, F.Cantanhede, F.Frank, R.Zhao, Z.Zarei, A.Butenschon, E.Matysik, J.Zimmermann, W.Strater, N.Sonnendecker, C.Kunze, G.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-70868-4
  • Primary Citation Related Structures: 
    9QNM, 9QT8, 9QV8, 9QVA, 9QYA, 9QYB, 9QYC

  • PubMed Abstract: 

    Polyethylene terephthalate (PET) plastic waste causes serious environmental pollution due to insufficient recycling rates. Enzymatic PET depolymerization offers a sustainable recycling strategy, but limited stability and activity of current PET-degrading enzymes restrict practical implementation. Here, we engineer Polyester Hydrolase Leipzig 7 (PHL7), a PET hydrolase from a compost metagenome, to enhance its stability and catalytic performance under recycling-relevant conditions. Using Rosetta PROSS-based computational design combined with rational mutagenesis, we introduce up to 24 mutations, generating variants with melting temperatures of 88-95 °C and over 110-fold higher activity in 0.1 M phosphate buffer compared to the parent enzyme. Benchmarking shows that the best variants (R4M6, R4M9, and R4M10) match or exceed the performance of established engineered PET hydrolases, including ICCG and LCC-A2, and approach that of TurboPETase across multiple conditions. Under high substrate loadings, the PHL7-R4 variants degrade 75-78% of 10% (w/w) PET within 24 h at 65 °C, outperforming ICCG, while an optimized variant R4M10-H185Y achieves up to 84% degradation of 20% (w/w) PET. X-ray structure determination and molecular dynamics simulations reveal key stabilizing and activity enhancing mechanisms. These engineered PHL7 variants represent robust biocatalysts for scalable enzymatic PET recycling.


  • Organizational Affiliation
    • Institute for Drug Discovery, Leipzig University, Leipzig, Germany.

Macromolecule Content 

  • Total Structure Weight: 58.15 kDa 
  • Atom Count: 4,747 
  • Modeled Residue Count: 522 
  • Deposited Residue Count: 534 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant
A, B
267compost metagenomeMutation(s): 24 
UniProt
Find proteins for A0AA82WPD4 (unidentified)
Explore A0AA82WPD4 
Go to UniProtKB:  A0AA82WPD4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WPD4
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free:  0.224 (Depositor), 0.225 (DCC) 
  • R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
  • R-Value Observed: 0.193 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.104α = 90
b = 73.732β = 97.2
c = 63.76γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European UnionState of Saxony, European Union's Just Transition Fund, grant nr 100704504
European Union (EU)European UnionHorizon 2020 research and innovation program, grant nr 887913 (ENZYCLE)

Revision History  (Full details and data files)

  • Version 1.0: 2026-05-27
    Type: Initial release