9QBN | pdb_00009qbn

Crystal structure of the polyester hydrolase Leipzig 7 (PHL7) mut3 variant with glycosylation by expression in Pichia pastoris (P_PHL7mut3)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 
    0.168 (Depositor), 0.169 (DCC) 
  • R-Value Work: 
    0.134 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 
    0.135 (Depositor) 

Starting Model: experimental
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Literature

Trade-Offs between Stability and Activity of Glycosylated and Non-Glycosylated Polyester Hydrolases PHL7 and PHL7mut3.

Fohler, L.Faschingeder, F.Leibetseder, L.Zhao, Z.Useini, A.Strater, N.Sonnendecker, C.Ewing, T.A.Moers, A.P.H.A.Werten, M.W.T.van Vliet, D.M.Julsing, M.K.Zimmermann, W.Striedner, G.

(2025) ACS ES T Eng 5: 2781-2791

  • DOI: https://doi.org/10.1021/acsestengg.5c00272
  • Primary Citation of Related Structures:  
    9QBN, 9QDE, 9QDV

  • PubMed Abstract: 

    Plastic pollution has become a global environmental challenge, driving interest in enzymatic polyethylene terephthalate (PET) recycling by using polyester hydrolases. In this study, we produced the PET-degrading enzyme PHL7 and its variant PHL7mut3 in Escherichia coli and Pichia pastoris (syn. Komagataella phaffii ) to investigate the impact of N-glycosylation on enzyme properties. While glycosylation upon expression in P. pastoris enhanced thermal stability, it reduced the catalytic activity of the enzymes, revealing a trade-off that adds complexity to the selection of the best-suited expression system. Additionally, we engineered P. pastoris to produce non-glycosylated enzyme variants by substituting the asparagine residues (N) at all three putative N-glycosylation sites with glutamine residues (Q). The non-glycosylated P. pastoris -produced enzymes showed a lower activity compared to those produced in E. coli , likely due to the differences in the amino acid sequence. The effects of glycosylation were less pronounced in PHL7mut3 than in PHL7, yet N-glycosylation strongly influenced the performance of both enzymes. We further demonstrate that the PET degradation performance of PHL7mut3 is less dependent on the buffer ionic strength than that of PHL7. The study emphasizes the need for the informed selection of a suitable expression host for polyester hydrolases to balance enzyme activity, thermostability, and production titer for applications in PET recycling.


  • Organizational Affiliation
    • Department of Biotechnology, Institute of Bioprocess Science and Engineering, BOKU University, Vienna 1190, Austria.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Polyester Hydrolase Leipzig 7 (PHL-7), catalysis-deficient S131A mutant265compost metagenomeMutation(s): 4 
UniProt
Find proteins for A0AA82WPD4 (unidentified)
Explore A0AA82WPD4 
Go to UniProtKB:  A0AA82WPD4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0AA82WPD4
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free:  0.168 (Depositor), 0.169 (DCC) 
  • R-Value Work:  0.134 (Depositor), 0.134 (DCC) 
  • R-Value Observed: 0.135 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.422α = 90
b = 63.997β = 90
c = 101.025γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
STARANISOdata scaling
XDSdata reduction
Cootmodel building
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union887913

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-10
    Type: Initial release
  • Version 1.1: 2025-12-03
    Changes: Database references