3ZCH

Ascorbate peroxidase W41A-H42M mutant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Probing the Conformational Mobility of the Active Site of Ascorbate Peroxidase

Guimero, A.Badyal, S.K.Leeks, T.Moody, P.C.E.Raven, E.L.

(2013) Dalton Trans 42: 3170

  • DOI: 10.1039/c2dt32455e
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We have previously demonstrated (Badyal et al., J. Biol. Chem., 2006, 281, 24512) that removal of the active site tryptophan (Trp41) in ascorbate peroxidase increases the conformational mobility of the distal histidine residue (His42) and that His42 ...

    We have previously demonstrated (Badyal et al., J. Biol. Chem., 2006, 281, 24512) that removal of the active site tryptophan (Trp41) in ascorbate peroxidase increases the conformational mobility of the distal histidine residue (His42) and that His42 coordinates to the iron in the oxidised W41A enzyme to give a 6-coordinate, low-spin peroxidase. In this work, we probe the conformational flexibility of the active site in more detail. We examine whether other residues (Cys, Tyr, Met) can also ligate to the heme at position 42; we find that introduction of other ligating amino acids created a cavity in the heme pocket, but that formation of 6-coordinate heme is not observed. In addition, we examine the role of Asn-71, which hydrogen bonds to His42 and tethers the distal histidine in the active site pocket; we find that removal of this hydrogen bond increases the proportion of low-spin heme. We suggest that, in addition to its well-known role in facilitating the reaction with peroxide, His42 also plays a role in defining the shape and folding of the active site pocket.


    Organizational Affiliation

    Department of Chemistry, University of Leicester, University Road, Leicester, LE1 9HN, England, UK.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ASCORBATE PEROXIDASEA261Glycine maxMutation(s): 2 
Gene Names: apx1
EC: 1.11.1.11
Find proteins for Q43758 (Glycine max)
Explore Q43758 
Go to UniProtKB:  Q43758
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
EPE
Query on EPE

Download CCD File 
A
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
C8 H18 N2 O4 S
JKMHFZQWWAIEOD-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.155 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 82.629α = 90
b = 82.629β = 90
c = 74.95γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-19
    Type: Initial release
  • Version 1.1: 2013-02-27
    Changes: Database references