1Y25

structure of mycobacterial thiol peroxidase Tpx


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structure of the inactive variant C60S of Mycobacterium tuberculosis thiol peroxidase

Stehr, M.Hecht, H.J.Jager, T.Flohe, L.Singh, M.

(2006) Acta Crystallogr D Biol Crystallogr 62: 563-567

  • DOI: https://doi.org/10.1107/S0907444906008249
  • Primary Citation of Related Structures:  
    1Y25

  • PubMed Abstract: 

    The genome of Mycobacterium tuberculosis encodes several peroxiredoxins (Prxs) thought to be active against organic and inorganic peroxides. The open reading frame Rv1932 encodes a 165-residue thiol peroxidase (Tpx), which belongs to the atypical 2-Cys peroxiredoxin family. The crystal structure of the C60S mutant of M. tuberculosis Tpx (MtTpx) crystallized in space group P3(1)21, with unit-cell parameters a = 106.08, b = 106.08, c = 65.33 A. The structure has been refined to an R value of 17.1% (R(free) = 24.9%) at 2.1 A resolution. MtTpx is structurally homologous to other peroxiredoxins, including the mycobacterial AhpC and AhpE. The inactive MtTpx C60S mutant structure closely resembles the structure of Streptococcus pneumoniae Tpx (SpTpx) and thus represents the reduced enzyme state. The mutated active-site serine is electrostatically linked to Arg130 and hydrogen bonded to Thr57, practically identical to the cysteine in SpTpx. A cocrystallized acetate molecule mimics the position of the substrate and interacts with Ser60, Arg130 and Thr57.


  • Organizational Affiliation

    Department GNA, GBF - Gesellschaft für Biotechnologische Forschung, Mascheroder Weg 1, D-38124 Braunschweig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Probable thiol peroxidase
A, B
165Mycobacterium tuberculosisMutation(s): 1 
Gene Names: Rv1932 tpx
EC: 1.11.1
UniProt
Find proteins for P9WG35 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WG35 
Go to UniProtKB:  P9WG35
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WG35
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.175 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 106.089α = 90
b = 106.089β = 90
c = 65.334γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-20
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2023-10-25
    Changes: Data collection, Refinement description