1IYN

Crystal structure of chloroplastic ascorbate peroxidase from tobacco plants and structural insights for its instability


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal structure of chloroplastic ascorbate peroxidase from tobacco plants and structural insights into its instability

Wada, K.Tada, T.Nakamura, Y.Ishikawa, T.Yabuta, Y.Yoshimura, K.Shigeoka, S.Nishimura, K.

(2003) J Biochem 134: 239-244

  • DOI: https://doi.org/10.1093/jb/mvg136
  • Primary Citation of Related Structures:  
    1IYN

  • PubMed Abstract: 

    Ascorbate peroxidase (APX) is a heme-containing protein that plays a central role in scavenging H(2)O(2) in higher plants. The structure of stromal APX (sAPX) was determined at 1.6 A to an R-factor of 19.1% and an R-free-factor of 22.3%. The electrostatic potential of the gamma-channel that connects the molecular surface of sAPX to the gamma-edge of heme was more positive than that of cytosolic APX (cAPX) from pea, so sAPX might bind more easily with ascorbate than cAPX. The overall structure of sAPX was similar to those of cAPX from pea and cytochrome c peroxidase (CCP) from yeast, with a substantial difference in a loop structure located in the vicinity of the heme. The side chain of Arg169 in sAPX corresponding to His169 in cAPX and His181 in CCP extended in the opposite direction from the heme, forming two hydrogen bonds with carbonyl groups in the loop structure. The rapid inactivation of sAPX might be due to the characteristic conformation of Arg169 owing to the loop structure of sAPX.


  • Organizational Affiliation

    Research Institute for Advanced Science and Technology, Osaka Prefecture University, Gakuen-cho 1-2, Sakai, Osaka 599-8570.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chloroplastic ascorbate peroxidase295Nicotiana tabacumMutation(s): 0 
EC: 1.11.1.11
UniProt
Find proteins for Q8LNY5 (Nicotiana tabacum)
Explore Q8LNY5 
Go to UniProtKB:  Q8LNY5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8LNY5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.188α = 90
b = 76.79β = 90
c = 98.776γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-03
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-10-25
    Changes: Data collection, Database references, Derived calculations, Refinement description