7ATJ

RECOMBINANT HORSERADISH PEROXIDASE C1A COMPLEX WITH CYANIDE AND FERULIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.203 
  • R-Value Observed: 0.160 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

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: 35005-35011

  • DOI: 10.1074/jbc.274.49.35005
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We have solved the x-ray structures of the binary horseradish peroxidase C-ferulic acid complex and the ternary horseradish peroxidase C-cyanide-ferulic acid complex to 2.0 and 1.45 A, respectively. Ferulic acid is a naturally occurring phenolic comp ...

    We have solved the x-ray structures of the binary horseradish peroxidase C-ferulic acid complex and the ternary horseradish peroxidase C-cyanide-ferulic acid complex to 2.0 and 1.45 A, respectively. Ferulic acid is a naturally occurring phenolic compound found in the plant cell wall and is an in vivo substrate for plant peroxidases. The x-ray structures demonstrate the flexibility and dynamic character of the aromatic donor binding site in horseradish peroxidase and emphasize the role of the distal arginine (Arg(38)) in both substrate oxidation and ligand binding. Arg(38) hydrogen bonds to bound cyanide, thereby contributing to the stabilization of the horseradish peroxidase-cyanide complex and suggesting that the distal arginine will be able to contribute with a similar interaction during stabilization of a bound peroxy transition state and subsequent O-O bond cleavage. The catalytic arginine is additionally engaged in an extensive hydrogen bonding network, which also includes the catalytic distal histidine, a water molecule and Pro(139), a proline residue conserved within the plant peroxidase superfamily. Based on the observed hydrogen bonding network and previous spectroscopic and kinetic work, a general mechanism of peroxidase substrate oxidation is proposed.


    Related Citations: 
    • 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
    • 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 Biol 4: 1032
    • Crystallization and preliminary X-ray studies of recombinant horseradish peroxidase.
      Henriksen, A., Gajhede, M., Baker, P., Smith, A.T., Burke, J.F.
      (1995) Acta Crystallogr D Biol Crystallogr 51: 121

    Organizational Affiliation

    Protein Structure Group, Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Kobenhavn O, Denmark. anette@jerne.ki.ku.dk



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEROXIDASE C1AA308Armoracia rusticanaMutation(s): 0 
Gene Names: PRXC1AHPRC1
EC: 1.11.1.7
Find proteins for P00433 (Armoracia rusticana)
Explore P00433 
Go to UniProtKB:  P00433
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
FER
Query on FER

Download CCD File 
A
3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID
C10 H10 O4
KSEBMYQBYZTDHS-HWKANZROSA-N
 Ligand Interaction
CA
Query on CA

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

Download CCD File 
A
CYANIDE ION
C N
XFXPMWWXUTWYJX-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.47 Å
  • R-Value Free: 0.203 
  • R-Value Observed: 0.160 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.868α = 90
b = 66.93β = 90
c = 119.017γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
SHELXL-97refinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2000-01-14
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Data collection, Refinement description
  • Version 1.4: 2019-11-27
    Changes: Database references