2OBI

Crystal structure of the Selenocysteine to Cysteine Mutant of human phospholipid hydroperoxide glutathione peroxidase (GPx4)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis for catalytic activity and enzyme polymerization of phospholipid hydroperoxide glutathione peroxidase-4 (GPx4).

Scheerer, P.Borchert, A.Krauss, N.Wessner, H.Gerth, C.Hohne, W.Kuhn, H.

(2007) Biochemistry 46: 9041-9049

  • DOI: https://doi.org/10.1021/bi700840d
  • Primary Citation of Related Structures:  
    2OBI

  • PubMed Abstract: 

    Phospholipid hydroperoxide glutathione peroxidase (GPx4) is a moonlighting selenoprotein, which has been implicated in anti-oxidative defense, sperm development, and cerebral embryogenesis. Among GPx-isoforms, GPx4 is unique because of its capability to reduce complex lipid hydroperoxides and its tendency toward polymerization, but the structural basis for these properties remained unclear. To address this, we solved the crystal structure of the catalytically active U46C mutant of human GPx4 to 1.55 A resolution. X-ray data indicated a monomeric protein consisting of four alpha-helices and seven beta-strands. GPx4 lacks a surface exposed loop domain, which appears to limit the accessibility of the active site of other GPx-isoforms, and these data may explain the broad substrate specificity of GPx4. The catalytic triad (C46, Q81, and W136) is localized at a flat impression of the protein surface extending into a surface exposed patch of basic amino acids (K48, K135, and R152) that also contains polar T139. Multiple mutations of the catalytic triad indicated its functional importance. Like the wild-type enzyme, the U46C mutant exhibits a strong tendency toward protein polymerization, which was prevented by reductants. Site-directed mutagenesis suggested involvement of the catalytic C46 and surface exposed C10 and C66 in polymer formation. In GPx4 crystals, these residues contact adjacent protein monomers.


  • Organizational Affiliation

    Institute of Biochemistry, University Medicine Berlin-Charité, Monbijoustr. 2, D-10117 Berlin, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Phospholipid hydroperoxide glutathione peroxidase (GPX4)183Homo sapiensMutation(s): 0 
Gene Names: GPX4
EC: 1.11.1.12 (PDB Primary Data), 1.11.1.9 (UniProt)
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P36969 (Homo sapiens)
Explore P36969 
Go to UniProtKB:  P36969
PHAROS:  P36969
GTEx:  ENSG00000167468 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP36969
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.165 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.362α = 90
b = 61.362β = 90
c = 113.891γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-09-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-08-30
    Changes: Data collection, Database references, Refinement description