2P5Q

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


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:  

  • 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 ho ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glutathione peroxidase 5
A, B, C, D
170Populus trichocarpa x Populus deltoidesMutation(s): 0 
Gene Names: GPX5
Find proteins for A3FNZ8 (Populus trichocarpa x Populus deltoides)
Go to Gene View: GPX5
Go to UniProtKB:  A3FNZ8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, C, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CD
Query on CD

Download SDF File 
Download CCD File 
A, B, C, D
CADMIUM ION
Cd
WLZRMCYVCSSEQC-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.178 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 221.665α = 90.00
b = 221.665β = 90.00
c = 48.142γ = 120.00
Software Package:
Software NamePurpose
DENZOdata reduction
MLPHAREphasing
MAR345dtbdata collection
PDB_EXTRACTdata extraction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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