1QGJ

ARABIDOPSIS THALIANA PEROXIDASE N


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Arabidopsis thaliana peroxidase N: structure of a novel neutral peroxidase.

Mirza, O.Henriksen, A.Ostergaard, L.Welinder, K.G.Gajhede, M.

(2000) Acta Crystallogr D Biol Crystallogr 56: 372-375

  • DOI: 10.1107/s0907444999016340
  • Primary Citation of Related Structures:  
    1QGJ

  • PubMed Abstract: 
  • The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C (HRP C) ...

    The structure of the neutral peroxidase from Arabidopsis thaliana (ATP N) has been determined to a resolution of 1.9 A and a free R value of 20.5%. ATP N has the expected characteristic fold of the class III peroxidases, with a C(alpha) r.m.s.d. of 0.82 A when compared with horseradish peroxidase C (HRP C). HRP C is 54% identical to ATP N in sequence. When the structures of four class III plant peroxidases are superimposed, the regions with structural differences are non-randomly distributed; all are located in one half of the molecule. The architecture of the haem pocket of ATP N is very similar to that of HRP C, in agreement with the low small-molecule substrate specificity of all class III peroxidases. The structure of ATP N suggests that the pH dependence of the substrate turnover will differ from that of HRP C owing to differences in polarity of the residues in the substrate-access channel. Since there are fewer hydrogen bonds to haem C17 propionate O atoms in ATP N than in HRP C, it is suggested that ATP N will lose haem more easily than HRP C. Unlike almost all other class III plant peroxidases, ATP N has a free cysteine residue at a similar position to the suggested secondary substrate-binding site in lignin peroxidase.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PEROXIDASE NA, B300Arabidopsis thalianaMutation(s): 0 
Gene Names: PER59P59At5g19890F28I16.40
EC: 1.11.1 (PDB Primary Data), 1.11.1.7 (UniProt)
UniProt
Find proteins for Q39034 (Arabidopsis thaliana)
Explore Q39034 
Go to UniProtKB:  Q39034
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.989α = 90
b = 87.457β = 90
c = 91.371γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-03-08
    Type: Initial release
  • Version 1.1: 2008-04-26
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance