9QYU | pdb_00009qyu

Crystal structure of leaf branch compost cutinase quintuple variant ICCG L50Y


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 
    0.184 (Depositor), 0.192 (DCC) 
  • R-Value Work: 
    0.149 (Depositor), 0.194 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Application of a Rational Crystal Contact Engineering Strategy on a Poly(ethylene terephthalate)-Degrading Cutinase.

Walla, B.Dietrich, A.M.Brames, E.Bischoff, D.Fritzsche, S.Castiglione, K.Janowski, R.Niessing, D.Weuster-Botz, D.

(2025) Bioengineering (Basel) 12

  • DOI: https://doi.org/10.3390/bioengineering12060561
  • Primary Citation of Related Structures:  
    9QYP, 9QYQ, 9QYR, 9QYS, 9QYT, 9QYU

  • PubMed Abstract: 

    Industrial biotechnology offers a potential ecological solution for PET recycling under relatively mild reaction conditions via enzymatic degradation, particularly using the leaf branch compost cutinase (LCC) quadruple mutant ICCG. To improve the efficient downstream processing of this biocatalyst after heterologous gene expression with a suitable production host, protein crystallization can serve as an effective purification/capture step. Enhancing protein crystallization was achieved in recent studies by introducing electrostatic (and aromatic) interactions in two homologous alcohol dehydrogenases ( Lb / Lk ADH) and an ene reductase ( Nsp ER1-L1,5) produced with Escherichia coli . In this study, ICCG, which is difficult to crystallize, was utilized for the application of crystal contact engineering strategies, resulting in ICCG mutant L50Y (ICCGY). Previously focused on the Lys-Glu interaction for the introduction of electrostatic interactions at crystal contacts, the applicability of the engineering strategy was extended here to an Arg-Glu interaction to increase crystallizability, as shown for ICCGY T110E. Furthermore, the rationale of the engineering approach is demonstrated by introducing Lys and Glu at non-crystal contacts or sites without potential interaction partners as negative controls. These resulting mutants crystallized comparably but not superior to the wild-type protein. As demonstrated by this study, crystal contact engineering emerges as a promising approach for rationally enhancing protein crystallization. This advancement could significantly streamline biotechnological downstream processing, offering a more efficient pathway for research and industry.


  • Organizational Affiliation

    Biochemical Engineering, Department of Energy and Process Engineering, TUM School of Engineering and Design, Technical University of Munich, Boltzmannstraße 15, 85748 Garching, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Leaf-branch compost cutinaseA [auth B]257uncultured bacteriumMutation(s): 1 
EC: 3.1.1.74 (PDB Primary Data), 3.1.1.101 (PDB Primary Data)
UniProt
Find proteins for G9BY57 (Unknown prokaryotic organism)
Explore G9BY57 
Go to UniProtKB:  G9BY57
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG9BY57
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free:  0.184 (Depositor), 0.192 (DCC) 
  • R-Value Work:  0.149 (Depositor), 0.194 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 96.65α = 90
b = 96.65β = 90
c = 73.71γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research Foundation (DFG)GermanyWE2715/14-2

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-02
    Type: Initial release
  • Version 1.1: 2025-07-09
    Changes: Database references