3PL1

Determination of the crystal structure of the pyrazinamidase from M.tuberculosis : a structure-function analysis for prediction resistance to pyrazinamide.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Pyrazinamidase of Mycobacterium tuberculosis: Insights into Natural and Acquired Resistance to Pyrazinamide.

Petrella, S.Gelus-Ziental, N.Maudry, A.Laurans, C.Boudjelloul, R.Sougakoff, W.

(2011) Plos One 6: e15785-e15785

  • DOI: 10.1371/journal.pone.0015785

  • PubMed Abstract: 
  • Pyrazinamidase (PncA) activates the first-line antituberculous drug pyrazinamide into pyrazinoic acid. The crystal structure of the Mycobacterium tuberculosis PncA protein has been determined, showing significant differences in the substrate binding ...

    Pyrazinamidase (PncA) activates the first-line antituberculous drug pyrazinamide into pyrazinoic acid. The crystal structure of the Mycobacterium tuberculosis PncA protein has been determined, showing significant differences in the substrate binding cavity when compared to the pyrazinamidases from Pyrococcus horikoshii and Acinetobacter baumanii. In M. tuberculosis, this region was found to hold a Fe(2+) ion coordinated by one aspartate and three histidines, one of them corresponding to His57 which is replaced by Asp in Mycobacterium bovis, a species naturally resistant to pyrazinamide. The binding cavity also contains a Cys138-Asp8-Lys96 motif evocating a cysteine-based catalytic mechanism. Mutants have been constructed and investigated by kinetic and thermal shift assays, highlighting the importance of protein folding and thermal stability in the pyrazinamidase activity.


    Organizational Affiliation

    Faculté de Médecine Pitié-Salpêtrière, UPMC Université Paris 6, ER 5, EA1541, Bactériologie-Hygiène, Paris, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PYRAZINAMIDASE/NICOTINAMIDASE PNCA (PZase)
A
186Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pncA
EC: 3.5.1.-
Find proteins for Q50575 (Mycobacterium tuberculosis)
Go to UniProtKB:  Q50575
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FE2
Query on FE2

Download SDF File 
Download CCD File 
A
FE (II) ION
Fe
CWYNVVGOOAEACU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.195 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 84.100α = 90.00
b = 84.100β = 90.00
c = 100.000γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-01-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-11-12
    Type: Structure summary