2GHK

Conformational mobility in the active site of a heme peroxidase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1074/jbc.M602602200
  • Primary Citation of Related Structures:  
    2GGN, 2GHC, 2GHD, 2GHE, 2GHH, 2GHK

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cytosolic ascorbate peroxidase 1A [auth X]261Glycine maxMutation(s): 0 
Gene Names: ascorbate peroxidase
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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.188 
  • R-Value Observed: 0.190 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.874α = 90
b = 80.874β = 90
c = 75.252γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
HKL-2000data reduction
REFMACrefinement
HKL-2000data 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: 2006-06-13
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Advisory, Refinement description
  • Version 1.4: 2024-02-14
    Changes: Advisory, Data collection, Database references, Derived calculations