1BGP

CRYSTAL STRUCTURE OF BARLEY GRAIN PEROXIDASE 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of barley grain peroxidase refined at 1.9-A resolution. A plant peroxidase reversibly inactivated at neutral pH.

Henriksen, A.Welinder, K.G.Gajhede, M.

(1998) J.Biol.Chem. 273: 2241-2248


  • PubMed Abstract: 
  • The crystal structure of the major peroxidase of barley grain (BP 1) has been solved by molecular replacement and phase combination and refined to an R-factor of 19.2% for all data between 38 and 1.9 A. The refined model includes amino acid residues ...

    The crystal structure of the major peroxidase of barley grain (BP 1) has been solved by molecular replacement and phase combination and refined to an R-factor of 19.2% for all data between 38 and 1.9 A. The refined model includes amino acid residues 1-309, one calcium ion, one sodium ion, iron-protoporphyrin IX, and 146 solvent molecules. BP 1 has the apparently unique property of being unable to catalyze the reaction with the primary substrate hydrogen peroxide to form compound I at pH values > 5, a feature investigated by obtaining crystal structure data at pH 5.5, 7.5, and 8.5. Structural comparison shows that the overall fold of inactive barley grain peroxidase at these pH values resembles that of both horseradish peroxidase C and peanut peroxidase. The key differences between the structures of active horseradish peroxidase C and inactive BP 1 include the orientation of the catalytic distal histidine, disruption of a hydrogen bond between this histidine and a conserved asparagine, and apparent substitution of calcium at the distal cation binding site with sodium at pH 7.5. These profound changes are a result of a dramatic structural rearrangement to the loop region between helices B and C. This is the first time that structural rearrangements linked to active site chemistry have been observed by crystallography in the peroxidase domain distal to heme.


    Organizational Affiliation

    Department of Physical Chemistry, University of Copenhagen, KĂžbenhavn O, Denmark. anette@jerne.ki.ku.dk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
BARLEY GRAIN PEROXIDASE
A
309Hordeum vulgareGene Names: Prx5
EC: 1.11.1.7
Find proteins for Q40069 (Hordeum vulgare)
Go to UniProtKB:  Q40069
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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

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Download CCD File 
A
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: 1.9 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.192 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 71.920α = 90.00
b = 105.060β = 90.00
c = 40.950γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
CCP4data scaling
X-PLORmodel building
X-PLORphasing
CCP4data reduction
X-PLORrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 1997-07-24 
  • Released Date: 1997-11-12 
  • Deposition Author(s): Henriksen, A.

Revision History 

  • Version 1.0: 1997-11-12
    Type: Initial release
  • Version 1.1: 2008-03-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance