6CRE

Dehaloperoxidase B in complex with 5-Br-ortho-guaiacol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Peroxidase versus Peroxygenase Activity: Substrate Substituent Effects as Modulators of Enzyme Function in the Multifunctional Catalytic Globin Dehaloperoxidase.

McGuire, A.H.Carey, L.M.de Serrano, V.Dali, S.Ghiladi, R.A.

(2018) Biochemistry 57: 4455-4468

  • DOI: https://doi.org/10.1021/acs.biochem.8b00540
  • Primary Citation of Related Structures:  
    6CH5, 6CH6, 6CKE, 6CO5, 6CRE

  • PubMed Abstract: 

    The dehaloperoxidase-hemoglobin (DHP) from the terebellid polychaete Amphitrite ornata is a multifunctional hemoprotein that catalyzes the oxidation of a wide variety of substrates, including halo/nitrophenols, haloindoles, and pyrroles, via peroxidase and/or peroxygenase mechanisms. To probe whether substrate substituent effects can modulate enzyme activity in DHP, we investigated its reactiviy against a panel of o-guaiacol substrates given their presence (from native/halogenated and non-native/anthropogenic sources) in the benthic environment that A. ornata inhabits. Using biochemical assays supported by spectroscopic, spectrometric, and structural studies, DHP was found to catalyze the H 2 O 2 -dependent oxidative dehalogenation of 4-haloguaiacols (F, Cl, and Br) to 2-methoxybenzoquinone (2-MeOBQ). 18 O labeling studies confirmed that O atom incorporation was derived exclusively from water, consistent with substrate oxidation via a peroxidase-based mechanism. The 2-MeOBQ product further reduced DHP to its oxyferrous state, providing a link between the substrate oxidation and O 2 carrier functions of DHP. Nonnative substrates resulted in polymerization of the initial substrate with varying degrees of oxidation, with 2-MeOBQ identified as a minor product. When viewed alongside the reactivity of previously studied phenolic substrates, the results presented here show that simple substituent effects can serve as functional switches between peroxidase and peroxygenase activities in this multifunctional catalytic globin. More broadly, when recent findings on DHP activity with nitrophenols and azoles are included, the results presented here further demonstrate the breadth of heterocyclic compounds of anthropogenic origin that can potentially disrupt marine hemoglobins or function as environmental stressors, findings that may be important when assessing the environmental impact of these pollutants (and their metabolites) on aquatic systems.


  • Organizational Affiliation

    Department of Chemistry , North Carolina State University , Raleigh , North Carolina 27695-8204 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.58 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.222α = 90
b = 66.188β = 90
c = 68.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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 StatesCHE-1150709

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-03
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description