2VUP | pdb_00002vup

Crystal structure of a type II tryparedoxin-dependant peroxidase from Trypanosoma brucei


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Structural and Mechanistic Insights Into Type II Trypanosomatid Tryparedoxin-Dependent Peroxidases.

Alphey, M.S.Konig, J.Fairlamb, A.H.

(2008) Biochem J 414: 375

  • DOI: https://doi.org/10.1042/BJ20080889
  • Primary Citation Related Structures: 
    2VUP

  • PubMed Abstract: 

    TbTDPX (Trypanosoma brucei tryparedoxin-dependent peroxidase) is a genetically validated drug target in the fight against African sleeping sickness. Despite its similarity to members of the GPX (glutathione peroxidase) family, TbTDPX2 is functional as a monomer, lacks a selenocysteine residue and relies instead on peroxidatic and resolving cysteine residues for catalysis and uses tryparedoxin rather than glutathione as electron donor. Kinetic studies indicate a saturable Ping Pong mechanism, unlike selenium-dependent GPXs, which display infinite K(m) and V(max) values. The structure of the reduced enzyme at 2.1 A (0.21 nm) resolution reveals that the catalytic thiol groups are widely separated [19 A (0.19 nm)] and thus unable to form a disulphide bond without a large conformational change in the secondary-structure architecture, as reported for certain plant GPXs. A model of the oxidized enzyme structure is presented and the implications for small-molecule inhibition are discussed.


  • Organizational Affiliation
    • Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, Scotland, UK.

Macromolecule Content 

  • Total Structure Weight: 21.14 kDa 
  • Atom Count: 1,409 
  • Modeled Residue Count: 164 
  • Deposited Residue Count: 190 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GLUTATHIONE PEROXIDASE-LIKE PROTEIN190Trypanosoma bruceiMutation(s): 1 
EC: 1.11.1.9
UniProt
Find proteins for Q869A6 (Trypanosoma brucei)
Explore Q869A6 
Go to UniProtKB:  Q869A6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ869A6
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.263 (Depositor), 0.258 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.204 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.26α = 90
b = 32.7β = 95.92
c = 58.31γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description