1KZM

Distal Heme Pocket Mutant (R38S/H42E) of Recombinant Horseradish Peroxidase C (HRP C).


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural analysis of the two horseradish peroxidase catalytic residue variants H42E and R38S/H42E: implications for the catalytic cycle.

Meno, K.Jennings, S.Smith, A.T.Henriksen, A.Gajhede, M.

(2002) Acta Crystallogr.,Sect.D 58: 1803-1812

  • Primary Citation of Related Structures:  4ATJ

  • PubMed Abstract: 
  • The crystal structures of horseradish peroxidase C (HRPC) active-site mutants H42E and R38S/H42E co-crystallized with benzhydroxamic acid (BHA) and ferulic acid (FA), respectively, have been solved. The 2.5 A crystal structure of the H42E-BHA complex ...

    The crystal structures of horseradish peroxidase C (HRPC) active-site mutants H42E and R38S/H42E co-crystallized with benzhydroxamic acid (BHA) and ferulic acid (FA), respectively, have been solved. The 2.5 A crystal structure of the H42E-BHA complex reveals that the side-chain O atoms of Glu42 occupy positions that are very similar to the positions of the two side-chain N atoms of the distal histidine in the wild-type HRPC-BHA structure. The mutation disturbs the hydrogen-bonding network extending from residue 42 to the distal calcium ion and results in the absence of the water molecule that is usually ligated to this ion in plant peroxidases. Consequently, the distal calcium ion is six- rather than seven-coordinated. In the 2.0 A R38S/H42E structure the position of Glu42 is different and no FA is observed in the distal haem pocket. This is a consequence of the absence of the Arg38 side chain, which limits the flexibility of the Glu42 side chain and modulates its acidity, making it unsuitable as a general acid-base catalyst in the reaction cycle. The water ligated to the distal calcium ion is present, showing that the wild-type distal hydrogen-bonding network is preserved. These results show why a glutamic acid residue can substitute for the conserved distal histidine in HRPC and that Arg38 plays a significant role in controlling the positioning and ionization state of the residue at position 42. Furthermore, these structures indicate that changes in the distal cavity are conveyed through the distal hydrogen-bonding network to the distal calcium site.


    Related Citations: 
    • The structures of the horseradish peroxidase C-ferulic acid complex and the ternary complex with cyanide suggest how peroxidases oxidize small phenolic substrates.
      Henriksen, A.,Smith, A.T.,Gajhede, M.
      (1999) J.Biol.Chem. 274: 35005
    • Crystal structure of horseradish peroxidase C at 2.15 A resolution.
      Gajhede, M.,Schuller, D.J.,Henriksen, A.,Smith, A.T.,Poulos, T.L.
      (1997) Nat.Struct.Mol.Biol. 12: 1032
    • Structural interactions between horseradish peroxidase C and the substrate benzhydroxamic acid determined by X-ray crystallography.
      Henriksen, A.,Schuller, D.J.,Meno, K.,Welinder, K.G.,Smith, A.T.,Gajhede, M.
      (1998) Biochemistry 37: 8054


    Organizational Affiliation

    Protein Structure Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peroxidase C1A
A
308Armoracia rusticanaGene Names: PRXC1A (HPRC1)
EC: 1.11.1.7
Find proteins for P00433 (Armoracia rusticana)
Go to UniProtKB:  P00433
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
HEM
Query on HEM

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

Download SDF File 
Download CCD File 
A
CACODYLATE ION
dimethylarsinate
C2 H6 As O2
OGGXGZAMXPVRFZ-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.168 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.400α = 90.00
b = 66.700β = 90.00
c = 117.100γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
SCALEPACKdata scaling
DENZOdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-09
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description