6ELW

High resolution structure of selenocysteine containing human GPX4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystal structure and functional characterization of selenocysteine-containing glutathione peroxidase 4 suggests an alternative mechanism of peroxide reduction.

Borchert, A.Kalms, J.Roth, S.R.Rademacher, M.Schmidt, A.Holzhutter, H.G.Kuhn, H.Scheerer, P.

(2018) Biochim Biophys Acta 1863: 1095-1107

  • DOI: 10.1016/j.bbalip.2018.06.006
  • Primary Citation of Related Structures:  
    6ELW

  • PubMed Abstract: 
  • Glutathione peroxidases (GPX) are anti-oxidative enzymes that reduce organic and inorganic hydroperoxides to the corresponding alcohols at the expense of reduced glutathione. The human genome involves eight GPX genes and five of them encode for selenocysteine-containing enzymes ...

    Glutathione peroxidases (GPX) are anti-oxidative enzymes that reduce organic and inorganic hydroperoxides to the corresponding alcohols at the expense of reduced glutathione. The human genome involves eight GPX genes and five of them encode for selenocysteine-containing enzymes. Among the human GPX-isoforms, GPX4 is unique since it is capable of reducing complex hydroperoxy ester lipids such as hydroperoxy phospholipids and hydroperoxy cholesterolesters. Using a number of genetically modified mouse strains the biological role of GPX4 has comprehensively characterized but the molecular enzymology is less well explored. This lack of knowledge is partly related to the fact that mammalian selenoproteins are not high-level expressed in conventional overexpression systems. To explore the structural and functional properties of human GPX4 we expressed this selenoprotein in a cysteine-auxotrophic E. coli strain using a semi-chemical expression strategy. The recombinant enzyme was purified in mg amounts from the bacterial lysate to electrophoretic homogeneity and characterized with respect to its protein-chemical and enzymatic properties. Its crystal structure was solved at 1.3 Å resolution and the X-ray data indicated a monomeric protein, which contains the catalytic selenium at the redox level of the seleninic acid. These data suggest an alternative reaction mechanism involving three different redox states (selenol, selenenic acid, seleninic acid) of the catalytically active selenocysteine.


    Organizational Affiliation

    Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charitéplatz 1, D-10117 Berlin, Germany. Electronic address: patrick.scheerer@charite.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Phospholipid hydroperoxide glutathione peroxidase, mitochondrialA192Homo sapiensMutation(s): 7 
Gene Names: GPX4
EC: 1.11.1.12
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens)
Explore P36969 
Go to UniProtKB:  P36969
PHAROS:  P36969
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36969
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A],
D [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SE7
Query on SE7
A L-PEPTIDE LINKINGC3 H7 N O4 SeSEC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.124 
  • R-Value Observed: 0.125 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 32.963α = 90
b = 69β = 115.12
c = 35.666γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB740
German Research FoundationGermanySFB1078
German Research FoundationGermanyKu961/11-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-20
    Type: Initial release
  • Version 1.1: 2018-07-04
    Changes: Data collection, Database references