6KY4

Crystal structure of Sulfiredoxin from Arabidopsis thaliana


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.249 

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This is version 1.3 of the entry. See complete history


Literature

The crystal structure of sulfiredoxin from Arabidopsis thaliana revealed a more robust antioxidant mechanism in plants.

Liu, M.Wang, J.Li, X.Sylvanno, M.J.Li, M.Zhang, M.Wang, M.

(2019) Biochem Biophys Res Commun 520: 347-352

  • DOI: https://doi.org/10.1016/j.bbrc.2019.10.034
  • Primary Citation of Related Structures:  
    6KY4

  • PubMed Abstract: 

    Typical 2-cysteine peroxiredoxins (2-Cys Prxs) are critical peroxidase sensors and could be deactivated by the hyperoxidation under oxidative stress. In plants, 2-Cys Prxs present at a high level in chloroplasts and are repaired by Sulfiredoxin. Whereas many studies have explored the mechanism of Sulfiredoxin from Homo sapiens (HsSrx), the molecular mechanism of Sulfiredoxin in plants with unique photosynthesis remains unclear. Here we report the crystal structure of Sulfiredoxin from Arabidopsis thaliana (AtSrx), which displayed a typical ParB/Srx fold with an ATP bound at a conservative nucleotide binding motif GCHR. Both the ADP binding pocket and the putative AtSrx-AtPrxA interaction surface of AtSrx are more positively charged comparing to HsSrx, suggesting a robust mechanism of AtSrx. These features illustrate the unique mechanisms of AtSrx, which are vital for figure out the strategies of plants to cope with oxidation stress.


  • Organizational Affiliation

    School of Life Sciences, Anhui University, Hefei, Anhui, 230601, China; Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, Hefei, Anhui, 230601, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfiredoxin, chloroplastic/mitochondrial112Arabidopsis thalianaMutation(s): 0 
Gene Names: SRXAt1g31170F28K20.12
EC: 1.8.98.2
UniProt
Find proteins for Q8GY89 (Arabidopsis thaliana)
Explore Q8GY89 
Go to UniProtKB:  Q8GY89
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GY89
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.294 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.249 
  • Space Group: P 43 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.544α = 90
b = 102.544β = 90
c = 102.544γ = 90
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-13
    Changes: Data collection, Database references
  • Version 1.3: 2023-11-22
    Changes: Data collection, Database references, Refinement description