4ILZ

Structural and kinetic study of an internal substrate binding site of dehaloperoxidase-hemoglobin A from Amphitrite ornata


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 

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


Literature

Structural and Kinetic Study of an Internal Substrate Binding Site in Dehaloperoxidase-Hemoglobin A from Amphitrite ornata.

Zhao, J.de Serrano, V.Zhao, J.Le, P.Franzen, S.

(2013) Biochemistry 52: 2427-2439

  • DOI: https://doi.org/10.1021/bi301307f
  • Primary Citation of Related Structures:  
    4FH6, 4FH7, 4ILZ

  • PubMed Abstract: 

    X-ray crystal structures of dehaloperoxidase-hemoglobin A (DHP A) from Amphitrite ornata soaked with substrate, 2,4,6-tribromophenol (2,4,6-TBP), in buffer solvent with added methanol (MeOH), 2-propanol (2-PrOH), and dimethyl sulfoxide (DMSO) reveal an internal substrate binding site deep in the distal pocket above the α-edge of the heme that is distinct from the previously determined internal inhibitor binding site. The peroxidase function of DHP A has most often been studied using 2,4,6-trichlorophenol (2,4,6-TCP) as a substrate analogue because of the low solubility of 2,4,6-TBP in an aqueous buffer solution. Previous studies at low substrate concentrations pointed to the binding of substrate 2,4,6-TCP at an external site near the exterior heme β- or δ-edge as observed in the class of heme peroxidases. Here we report that the turnover frequencies of both substrates 2,4,6-TCP and 2,4,6-TBP deviate from Michaelis-Menten kinetics at high concentrations. The turnover frequency reaches a maximum in the range of 1400-1700 μM, with a decrease in rate at higher concentrations that is both substrate- and solvent-dependent. The X-ray crystal structure is consistent with the presence of an internal active site above the heme α-edge, in which the substrate would be oxidized in two consecutive steps inside the enzyme, followed by attack by H2O via a water channel in the protein. The physiological role of the internal site may involve interactions with any of a number of aromatic toxins found in benthic ecosystems where A. ornata resides.


  • Organizational Affiliation

    Department of Chemistry, North Carolina State University, Raleigh, NC 27695, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Dehaloperoxidase A
A, B
137Amphitrite ornataMutation(s): 0 
Gene Names: dhpA
UniProt
Find proteins for Q9NAV8 (Amphitrite ornata)
Explore Q9NAV8 
Go to UniProtKB:  Q9NAV8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NAV8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

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

Download Ideal Coordinates CCD File 
M [auth A]2,4,6-TRIBROMOPHENOL
C6 H3 Br3 O
BSWWXRFVMJHFBN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A],
P [auth B],
Q [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
IPA
Query on IPA

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
J [auth A]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A]
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
OXY
Query on OXY

Download Ideal Coordinates CCD File 
N [auth A]OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.243 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.589α = 90
b = 67.184β = 90
c = 68.91γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-27
    Type: Initial release
  • Version 1.1: 2013-04-17
    Changes: Database references
  • Version 1.2: 2013-04-24
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description