1Y25

structure of mycobacterial thiol peroxidase Tpx

• PDB DOI: https://doi.org/10.2210/pdb1Y25/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-11-20 Released: 2005-11-20 
• Deposition Author(s): Stehr, M., Hoffmann, B., Jger, T., Singh, M., Hecht, H.J.

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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 

Starting Model: experimental

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

• PubMed: 16627951 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 33.94 kDa 
• Atom Count: 2,754 
• Modelled Residue Count: 330 
• Deposited Residue Count: 330 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable thiol peroxidase	A, B	165	Mycobacterium tuberculosis	Mutation(s): 1  Gene Names: Rv1932 tpx EC: 1.11.1 (PDB Primary Data), 1.11.1.24 (UniProt)
UniProt
Find proteins for P9WG35 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WG35  Go to UniProtKB:  P9WG35

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	C [auth A], D [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

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 = 106.089	α = 90
b = 106.089	β = 90
c = 65.334	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-11-20 
Deposition Author(s): Stehr, M., Hoffmann, B., Jger, T., Singh, M., Hecht, H.J.

Revision History  

• 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