8Q21 | pdb_00008q21

Crystal structure of Vanadium-dependent haloperoxidase R425S mutant (A. marina)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Unraveling the molecular basis of substrate specificity and halogen activation in vanadium-dependent haloperoxidases.

Zeides, P.Bellmann-Sickert, K.Zhang, R.Seel, C.J.Most, V.Schoeder, C.T.Groll, M.Gulder, T.

(2025) Nat Commun 16: 2083-2083

  • DOI: https://doi.org/10.1038/s41467-025-57023-1
  • Primary Citation of Related Structures:  
    8Q20, 8Q21, 8Q22

  • PubMed Abstract: 

    Vanadium-dependent haloperoxidases (VHPOs) are biotechnologically valuable and operationally versatile biocatalysts. VHPOs share remarkable active-site structural similarities yet display variable reactivity and selectivity. The factors dictating substrate specificity and, thus, a general understanding of VHPO reaction control still need to be discovered. This work's strategic single-point mutation in the cyanobacterial bromoperoxidase AmVHPO facilitates a selectivity switch to allow aryl chlorination. This mutation induces loop formation that interacts with the neighboring protein monomer, creating a tunnel to the active sites. Structural analysis of the substrate-R425S-mutant complex reveals a substrate-binding site at the interface of two adjacent units. There, residues Glu139 and Phe401 interact with arenes, extending the substrate residence time close to the vanadate cofactor and stabilizing intermediates. Our findings validate the long-debated existence of direct substrate binding and provide a detailed VHPO mechanistic understanding. This work will pave the way for a broader application of VHPOs in diverse chemical processes.


  • Organizational Affiliation
    • Biomimetic Catalysis, Catalysis Research Center, TUM School of Natural Sciences, Technical University of Munich, Garching, Germany.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vanadium-dependent bromoperoxidase, putative666Acaryochloris marinaMutation(s): 1 
Gene Names: AM1_4975
UniProt
Find proteins for B0C4R0 (Acaryochloris marina (strain MBIC 11017))
Explore B0C4R0 
Go to UniProtKB:  B0C4R0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupB0C4R0
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.233 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.220 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: F 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 306.74α = 90
b = 306.74β = 90
c = 306.74γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Structure summary
  • Version 1.2: 2025-03-12
    Changes: Database references