8S6C | pdb_00008s6c

Crystal structure of Cyanobacterium TDX16 peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 
    0.188 (Depositor), 0.191 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: in silico
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Biochemical and Structural Characterisation of a Bacterial Lactoperoxidase.

Pecanac, O.Martin, C.Savino, S.Rozeboom, H.J.Fraaije, M.W.Loncar, N.

(2025) Chembiochem 26: e202400713-e202400713

  • DOI: https://doi.org/10.1002/cbic.202400713
  • Primary Citation of Related Structures:  
    8S6C

  • PubMed Abstract: 

    Peroxidases belong to a group of enzymes that are widely found in animals, plants and microorganisms. These enzymes are effective biocatalysts for a wide range of oxidations on various substrates. This work presents a biochemical and structural characterization of a novel heme-containing peroxidase from Cyanobacterium sp. TDX16, CyanoPOX. This cyanobacterial enzyme was successfully overexpressed in Escherichia coli as a soluble, heme-containing monomeric enzyme. Although CyanoPOX shares relatively low sequence identity (37 %) with bovine lactoperoxidase, it displays comparable biochemical properties. CyanoPOX is most stable and active in slightly acidic conditions (pH 6-6.5) and moderately thermostable (melting temperature around 48 °C). Several compounds that are typical substrates for mammalian lactoperoxidases were tested to establish the catalytic potential of CyanoPOX. Potassium iodide showed the highest catalytic efficiency (126 mM -1  s -1 ), while various aromatic compounds were also readily converted. Structural elucidation of CyanoPOX confirmed the presence of a non-covalently bound b-type heme cofactor that is situated in the central core of the protein. Except for a highly similar overall structure, CyanoPOX also has a conserved active site pocket when compared with mammalian lactoperoxidases. Due to its catalytic properties and high expression in a bacterial host, this newly discovered peroxidase shows promise for applications.


  • Organizational Affiliation
    • GECCO Biotech, Zernikepark 6, 9747 AN, Groningen, The Netherlands.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lactoperoxidase528cyanobacterium TDX16Mutation(s): 0 
EC: 1.11.1.7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM (Subject of Investigation/LOI)
Query on HEM

Download Ideal Coordinates CCD File 
B [auth A]PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
C [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free:  0.188 (Depositor), 0.191 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.667α = 90
b = 72.541β = 95.85
c = 56.203γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Union (EU)European Union--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2025-02-05
    Changes: Database references