7PL0

Crystal structure of a DyP-type peroxidase 5G5 variant from Bacillus subtilis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Loops around the Heme Pocket Have a Critical Role in the Function and Stability of Bs DyP from Bacillus subtilis .

Rodrigues, C.F.Borges, P.T.Scocozza, M.F.Silva, D.Taborda, A.Brissos, V.Frazao, C.Martins, L.O.

(2021) Int J Mol Sci 22

  • DOI: https://doi.org/10.3390/ijms221910862
  • Primary Citation of Related Structures:  
    7PKX, 7PL0

  • PubMed Abstract: 

    Bacillus subtilis   Bs DyP belongs to class I of the dye-decolorizing peroxidase (DyP) family of enzymes and is an interesting biocatalyst due to its high redox potential, broad substrate spectrum and thermostability. This work reports the optimization of Bs DyP using directed evolution for improved oxidation of 2,6-dimethoxyphenol, a model lignin-derived phenolic. After three rounds of evolution, one variant was identified displaying 7-fold higher catalytic rates and higher production yields as compared to the wild-type enzyme. The analysis of X-ray structures of the wild type and the evolved variant showed that the heme pocket is delimited by three long conserved loop regions and a small α helix where, incidentally, the mutations were inserted in the course of evolution. One loop in the proximal side of the heme pocket becomes more flexible in the evolved variant and the size of the active site cavity is increased, as well as the width of its mouth, resulting in an enhanced exposure of the heme to solvent. These conformational changes have a positive functional role in facilitating electron transfer from the substrate to the enzyme. However, they concomitantly resulted in decreasing the enzyme's overall stability by 2 kcal mol -1 , indicating a trade-off between functionality and stability. Furthermore, the evolved variant exhibited slightly reduced thermal stability compared to the wild type. The obtained data indicate that understanding the role of loops close to the heme pocket in the catalysis and stability of DyPs is critical for the development of new and more powerful biocatalysts: loops can be modulated for tuning important DyP properties such as activity, specificity and stability.


  • Organizational Affiliation

    Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av da República, 2780-157 Oeiras, Portugal.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Deferrochelatase/peroxidase
A, B, C, D
416Bacillus subtilisMutation(s): 3 
Gene Names: B4417_2151CFD21_01545
EC: 1.11.1 (PDB Primary Data), 4.98.1.1 (UniProt)
UniProt
Find proteins for P39597 (Bacillus subtilis (strain 168))
Explore P39597 
Go to UniProtKB:  P39597
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP39597
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.852α = 90
b = 114.76β = 104
c = 116.819γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
H2020 Marie Curie Actions of the European CommissionUnited KingdomB-LigZymes H2020-MSCA-RISE 2018
Foundation for Science and Technology (FCT)United KingdomPTDC/BII-BBF/29564/2017
Foundation for Science and Technology (FCT)United KingdomPTDC/BBBEBB/0122/2014

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-27
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description