2GHE

Conformational mobility in the active site of a heme peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Conformational Mobility in the Active Site of a Heme Peroxidase.

Badyal, S.K.Joyce, M.G.Sharp, K.H.Seward, H.E.Mewies, M.Basran, J.Macdonald, I.K.Moody, P.C.E.Raven, E.L.

(2006) J.Biol.Chem. 281: 24512-24520

  • DOI: 10.1074/jbc.M602602200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Conformational mobility of the distal histidine residue has been implicated for several different heme peroxidase enzymes, but unambiguous structural evidence is not available. In this work, we present mechanistic, spectroscopic, and structural evide ...

    Conformational mobility of the distal histidine residue has been implicated for several different heme peroxidase enzymes, but unambiguous structural evidence is not available. In this work, we present mechanistic, spectroscopic, and structural evidence for peroxide- and ligand-induced conformational mobility of the distal histidine residue (His-42) in a site-directed variant of ascorbate peroxidase (W41A). In this variant, His-42 binds "on" to the heme in the oxidized form, duplicating the active site structure of the cytochromes b but, in contrast to the cytochromes b, is able to swing "off" the iron during catalysis. This conformational flexibility between the on and off forms is fully reversible and is used as a means to overcome the inherently unreactive nature of the on form toward peroxide, so that essentially complete catalytic activity is maintained. Contrary to the widely adopted view of heme enzyme catalysis, these data indicate that strong coordination of the distal histidine to the heme iron does not automatically undermine catalytic activity. The data add a new dimension to our wider appreciation of structure/activity correlations in other heme enzymes.


    Organizational Affiliation

    Department of Chemistry, Henry Wellcome Building, University of Leicester, University Road, Leicester LE1 7RH, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
cytosolic ascorbate peroxidase 1
X
261Glycine maxMutation(s): 1 
Gene Names: apx1 (553156)
EC: 1.11.1.11
Find proteins for Q43758 (Glycine max)
Go to UniProtKB:  Q43758
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
X
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

Download SDF File 
Download CCD File 
X
PROTOPORPHYRIN IX CONTAINING FE
HEME
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.180 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 82.003α = 90.00
b = 82.003β = 90.00
c = 75.012γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
MOSFLMdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-18
    Type: Refinement description