1XVQ | pdb_00001xvq

Crystal structure of thiol peroxidase from Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 
    0.225 (Depositor), 0.220 (DCC) 
  • R-Value Work: 
    0.203 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 1XVQ

This is version 1.4 of the entry. See complete history

Literature

Functional and Structural Characterization of a Thiol Peroxidase from Mycobacterium tuberculosis.

Rho, B.S.Hung, L.W.Holton, J.M.Vigil, D.Kim, S.I.Park, M.S.Terwilliger, T.C.Pedelacq, J.D.

(2006) J Mol Biology 361: 850-863

  • DOI: https://doi.org/10.1016/j.jmb.2006.05.076
  • Primary Citation Related Structures: 
    1XVQ

  • PubMed Abstract: 

    A thiol peroxidase (Tpx) from Mycobacterium tuberculosis was functionally analyzed. The enzyme shows NADPH-linked peroxidase activity using a thioredoxin-thioredoxin reductase system as electron donor, and anti-oxidant activity in a thiol-dependent metal-catalyzed oxidation system. It reduces H2O2, t-butyl hydroperoxide, and cumene hydroperoxide, and is inhibited by sulfhydryl reagents. Mutational studies revealed that the peroxidatic (Cys60) and resolving (Cys93) cysteine residues are critical amino acids for catalytic activity. The X-ray structure determined to a resolution of 1.75 A shows a thioredoxin fold similar to that of other peroxiredoxin family members. Superposition with structural homologues in oxidized and reduced forms indicates that the M. tuberculosis Tpx is a member of the atypical two-Cys peroxiredoxin family. In addition, the short distance that separates the Calpha atoms of Cys60 and Cys93 and the location of these cysteine residues in unstructured regions may indicate that the M. tuberculosis enzyme is oxidized, though the side-chain of Cys60 is poorly visible. It is solely in the reduced Streptococcus pneumoniae Tpx structure that both residues are part of two distinct helical segments. The M. tuberculosis Tpx is dimeric both in solution and in the crystal structure. Amino acid residues from both monomers delineate the active site pocket.


  • Organizational Affiliation
    • Bioscience Division, MS M888, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.

Macromolecule Content 

  • Total Structure Weight: 18.39 kDa 
  • Atom Count: 1,304 
  • Modeled Residue Count: 160 
  • Deposited Residue Count: 175 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
thiol peroxidase175Mycobacterium tuberculosisMutation(s): 1 
Gene Names: 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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WG35
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
  • R-Value Work:  0.203 (Depositor), 0.198 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.555α = 90
b = 64.555β = 90
c = 196.788γ = 120
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2004-12-07
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description