3DWV

Glutathione peroxidase-type tryparedoxin peroxidase, oxidized form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.128 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural basis for a distinct catalytic mechanism in Trypanosoma brucei tryparedoxin peroxidase.

Melchers, J.Diechtierow, M.Feher, K.Sinning, I.Tews, I.Krauth-Siegel, R.L.Muhle-Goll, C.

(2008) J Biol Chem 283: 30401-30411

  • DOI: 10.1074/jbc.M803563200
  • Primary Citation of Related Structures:  
    2RM5, 2RM6, 3DWV

  • PubMed Abstract: 
  • Trypanosoma brucei, the causative agent of African sleeping sickness, encodes three cysteine homologues (Px I-III) of classical selenocysteine-containing glutathione peroxidases. The enzymes obtain their reducing equivalents from the unique trypanothione (bis(glutathionyl)spermidine)/tryparedoxin system ...

    Trypanosoma brucei, the causative agent of African sleeping sickness, encodes three cysteine homologues (Px I-III) of classical selenocysteine-containing glutathione peroxidases. The enzymes obtain their reducing equivalents from the unique trypanothione (bis(glutathionyl)spermidine)/tryparedoxin system. During catalysis, these tryparedoxin peroxidases cycle between an oxidized form with an intramolecular disulfide bond between Cys(47) and Cys(95) and the reduced peroxidase with both residues in the thiol state. Here we report on the three-dimensional structures of oxidized T. brucei Px III at 1.4A resolution obtained by x-ray crystallography and of both the oxidized and the reduced protein determined by NMR spectroscopy. Px III is a monomeric protein unlike the homologous poplar thioredoxin peroxidase (TxP). The structures of oxidized and reduced Px III are essentially identical in contrast to what was recently found for TxP. In Px III, Cys(47), Gln(82), and Trp(137) do not form the catalytic triad observed in the selenoenzymes, and related proteins and the latter two residues are unaffected by the redox state of the protein. The mutational analysis of three conserved lysine residues in the vicinity of the catalytic cysteines revealed that exchange of Lys(107) against glutamate abrogates the reduction of hydrogen peroxide, whereas Lys(97) and Lys(99) play a crucial role in the interaction with tryparedoxin.


    Organizational Affiliation

    Department of Structure and Biocomputing, EMBL, 69117 Heidelberg, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutathione peroxidase-like proteinA, B187Trypanosoma bruceiMutation(s): 1 
Gene Names: gpx3Tb927.7.1140
EC: 1.11.1.9
UniProt
Find proteins for Q869A5 (Trypanosoma brucei)
Explore Q869A5 
Go to UniProtKB:  Q869A5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ869A5
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.41 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.116 
  • R-Value Observed: 0.128 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.81α = 90
b = 105.864β = 100.48
c = 42.738γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
PDB_EXTRACTdata extraction
DNAdata collection
HKL-2000data reduction
MOLREPphasing
ARP/wARPmodel building
SHELXL-97refinement

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-08-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-12-26
    Changes: Database references
  • Version 1.3: 2017-10-25
    Changes: Refinement description
  • Version 1.4: 2021-11-10
    Changes: Database references