8DOG | pdb_00008dog

Dehaloperoxidase B in complex with Bisphenol E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 
    0.172 (Depositor), 0.176 (DCC) 
  • R-Value Work: 
    0.126 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Oxidation of bisphenol A (BPA) and related compounds by the multifunctional catalytic globin dehaloperoxidase.

Yun, D.de Serrano, V.Ghiladi, R.A.

(2023) J Inorg Biochem 238: 112020-112020

  • DOI: https://doi.org/10.1016/j.jinorgbio.2022.112020
  • Primary Citation Related Structures: 
    8DOG, 8DOH, 8DOI, 8DOJ

  • PubMed Abstract: 

    Dehaloperoxidase (DHP) from the marine polychaete Amphitrite ornata is a multifunctional enzyme that possesses peroxidase, peroxygenase, oxidase and oxygenase activities. Herein, we investigated the reactivity of DHP B with bisphenol A (BPA) and related compounds (bisphenol E, bisphenol F, tetrachlorobisphenol A, 2,2'-biphenol, 3,3'-biphenol, 4,4'-biphenol, and 3,3'-dibromo-4,4'-biphenol). As a previously unknown substrate for DHP B, BPA (as a representative substrate) is an endocrine disruptor widely used in polycarbonate and epoxy resins, thus resulting in human exposure. Reactivity studies with these substrates were investigated using high performance liquid chromatography (HPLC), and their corresponding oxidation products were determined by mass spectrometry (GC-MS/ LC-MS). BPA undergoes oxidation in the presence of DHP B and hydrogen peroxide yielding two cleavage products (4-isopropenylphenol and 4-(2-hydroxypropan-2-yl)phenol), and oligomers with varying degrees of oxidation. 18 O-labeling studies confirmed that the O-atom incorporated into the products was derived exclusively from water, consistent with substrate oxidation via a peroxidase-based mechanism. The X-ray crystal structures of DHP bound with bisphenol E (1.48 Å), bisphenol F (1.75 Å), 2,2'-biphenol (1.90 Å) and 3,3'-biphenol (1.30 Å) showed substrate binding sites are in the distal pocket of the heme cofactor, similar to other previously studied DHP substrates. Stopped-flow UV-visible spectroscopy was utilized to investigate the mechanistic details and enzyme oxidation states during substrate turnover, and a reaction mechanism is proposed. The data presented here strongly suggest that DHP B can catalyze the oxidation of bisphenols and biphenols, thus providing evidence of how infaunal invertebrates can contribute to the biotransformation of these marine pollutants.


  • Organizational Affiliation
    • Department of Chemistry, North Carolina State University, Raleigh, NC 27695-8204, United States.

Macromolecule Content 

  • Total Structure Weight: 32.96 kDa 
  • Atom Count: 2,920 
  • Modeled Residue Count: 274 
  • Deposited Residue Count: 274 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Dehaloperoxidase B
A, B
137Amphitrite ornataMutation(s): 0 
UniProt
Find proteins for Q9NAV7 (Amphitrite ornata)
Explore Q9NAV7 
Go to UniProtKB:  Q9NAV7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NAV7
Sequence Annotations
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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
C [auth A],
I [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
H48

Query on H48



Download:Ideal Coordinates CCD File
D [auth A],
J [auth B]
4-[1-(4-hydroxyphenyl)ethyl]phenol
C14 H14 O2
HCNHNBLSNVSJTJ-UHFFFAOYSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
H [auth A]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free:  0.172 (Depositor), 0.176 (DCC) 
  • R-Value Work:  0.126 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.827α = 90
b = 67.344β = 90
c = 67.656γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-02
    Type: Initial release
  • Version 1.1: 2022-12-07
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description