2P5R

Crystal structure of the poplar glutathione peroxidase 5 in the oxidized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.218 

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This is version 1.3 of the entry. See complete history


Literature

Crystal Structures of a Poplar Thioredoxin Peroxidase that Exhibits the Structure of Glutathione Peroxidases: Insights into Redox-driven Conformational Changes.

Koh, C.S.Didierjean, C.Navrot, N.Panjikar, S.Mulliert, G.Rouhier, N.Jacquot, J.P.Aubry, A.Shawkataly, O.Corbier, C.

(2007) J Mol Biol 370: 512-529

  • DOI: 10.1016/j.jmb.2007.04.031
  • Primary Citation of Related Structures:  
    2P5R, 2P5Q

  • PubMed Abstract: 
  • Glutathione peroxidases (GPXs) are a group of enzymes that regulate the levels of reactive oxygen species in cells and tissues, and protect them against oxidative damage. Contrary to most of their counterparts in animal cells, the higher plant GPX homologues identified so far possess cysteine instead of selenocysteine in their active site ...

    Glutathione peroxidases (GPXs) are a group of enzymes that regulate the levels of reactive oxygen species in cells and tissues, and protect them against oxidative damage. Contrary to most of their counterparts in animal cells, the higher plant GPX homologues identified so far possess cysteine instead of selenocysteine in their active site. Interestingly, the plant GPXs are not dependent on glutathione but rather on thioredoxin as their in vitro electron donor. We have determined the crystal structures of the reduced and oxidized form of Populus trichocarpaxdeltoides GPX5 (PtGPX5), using a selenomethionine derivative. PtGPX5 exhibits an overall structure similar to that of the known animal GPXs. PtGPX5 crystallized in the assumed physiological dimeric form, displaying a pseudo ten-stranded beta sheet core. Comparison of both redox structures indicates that a drastic conformational change is necessary to bring the two distant cysteine residues together to form an intramolecular disulfide bond. In addition, a computer model of a complex of PtGPX5 and its in vitro recycling partner thioredoxin h1 is proposed on the basis of the crystal packing of the oxidized form enzyme. A possible role of PtGPX5 as a heavy-metal sink is also discussed.


    Organizational Affiliation

    LCM3B, Equipe Biocristallographie, UMR 7036 CNRS-UHP, Faculté des Sciences et Techniques, Nancy Université, BP 239, 54506 Vandoeuvre-lès-Nancy, France.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutathione peroxidase 5A, B170Populus trichocarpa x Populus deltoidesMutation(s): 0 
Gene Names: PtGPX5GPX5
EC: 1.11.1
Find proteins for A3FNZ8 (Populus trichocarpa x Populus deltoides)
Explore A3FNZ8 
Go to UniProtKB:  A3FNZ8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.218 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.58α = 90
b = 71.58β = 90
c = 117.82γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
MAR345dtbdata collection
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-07-24
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description