2WD4 | pdb_00002wd4

Ascorbate Peroxidase as a heme oxygenase: w41A variant product with t-butyl peroxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 
    0.216 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.190 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Evidence for Heme Oxygenase Activity in a Heme Peroxidase.

Raven, E.L.Badyal, S.K.Eaton, G.Mistry, S.Pipirou, Z.Basran, J.Metcalfe, C.L.Gumiero, A.Handa, S.Moody, P.C.E.

(2009) Biochemistry 48: 4738

  • DOI: https://doi.org/10.1021/bi900118j
  • Primary Citation Related Structures: 
    2WD4

  • PubMed Abstract: 

    The heme peroxidase and heme oxygenase enzymes share a common heme prosthetic group but catalyze fundamentally different reactions, the first being H(2)O(2)-dependent oxidation of substrate using an oxidized Compound I intermediate, and the second O(2)-dependent degradation of heme. It has been proposed that these enzymes utilize a common reaction intermediate, a ferric hydroperoxide species, that sits at a crossroads in the mechanism and beyond which there are two mutually exclusive mechanistic pathways. Here, we present evidence to support this proposal in a heme peroxidase. Hence, we describe kinetic data for a variant of ascorbate peroxidase (W41A) which reacts slowly with tert-butyl hydroperoxide and does not form the usual peroxidase Compound I intermediate; instead, structural data show that a product is formed in which the heme has been cleaved at the alpha-meso position, analogous to the heme oxygenase mechanism. We interpret this to mean that the Compound I (peroxidase) pathway is shut down, so that instead the reaction intermediate diverts through the alternative (heme oxygenase) route. A mechanism for formation of the product is proposed and discussed in the light of what is known about the heme oxygenase reaction mechanism.


  • Organizational Affiliation
    • Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, UK.

Macromolecule Content 

  • Total Structure Weight: 29.16 kDa 
  • Atom Count: 2,219 
  • Modeled Residue Count: 248 
  • Deposited Residue Count: 261 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
ASCORBATE PEROXIDASE261Glycine maxMutation(s): 1 
EC: 1.11.1.11
UniProt
Find proteins for Q43758 (Glycine max)
Explore Q43758 
Go to UniProtKB:  Q43758
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ43758
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TBV

Query on TBV



Download:Ideal Coordinates CCD File
E [auth A]3-[2-[[3-(2-CARBOXYETHYL)-5-[[3-ETHENYL-4-METHYL-5-[(2-METHYLPROPAN-2-YL)OXY]-1H-PYRROL-2-YL]METHYL]-4-METHYL-1H-PYRROL -2-YL]METHYL]-5-[(Z)-(4-ETHENYL-3-METHYL-5-OXO-PYRROL-2-YLIDENE)METHYL]-4-METHYL-1H-PYRROL-3-YL]PROPANOIC ACID
C37 H46 N4 O6
JDQNAGCTUKHXGS-MWLSYYOVSA-N
SO4

Query on SO4



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

Query on FE



Download:Ideal Coordinates CCD File
B [auth A]FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free:  0.216 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.190 (Depositor), 0.189 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.067α = 90
b = 82.067β = 90
c = 75.137γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
CCP4phasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-04-07
    Type: Initial release
  • Version 1.1: 2016-05-11
    Changes: Structure summary, Version format compliance
  • Version 1.2: 2019-05-08
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary