5SYI

Structure of D141A variant of B. pseudomallei KatG complexed with INH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Binding of the antitubercular pro-drug isoniazid in the heme access channel of catalase-peroxidase (KatG). A combined structural and metadynamics investigation.

Vidossich, P.Loewen, P.C.Carpena, X.Fiorin, G.Fita, I.Rovira, C.

(2014) J Phys Chem B 118: 2924-2931

  • DOI: 10.1021/jp4123425
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Isonicotinic acid hydrazide (isoniazid or INH) is a front line antitubercular pro-drug that is converted to its active form, isonicotinyl-NAD, by the bacterial catalase-peroxidase KatG. Understanding the role of KatG in the INH activation process has ...

    Isonicotinic acid hydrazide (isoniazid or INH) is a front line antitubercular pro-drug that is converted to its active form, isonicotinyl-NAD, by the bacterial catalase-peroxidase KatG. Understanding the role of KatG in the INH activation process has been hampered by a lack of knowledge of the actual drug binding site. In this work, we have investigated the binding of INH in the main access channel of KatG with a combination of molecular dynamics, using an enhanced-sampling technique (metadynamics), X-ray crystallography, and site-directed mutagenesis. The metadynamics simulations show that there are several weak drug binding sites along the access channel. Moreover, the simulations evidence that complete entrance to the heme active site is impeded by an aspartate residue (D141) located above the heme. This has been confirmed by structural and functional analysis of the D141A mutant, leading to the first X-ray crystallography evidence of INH at the heme access channel.


    Organizational Affiliation

    Unitat de Química Física, Departament de Química, Universitat Autònoma de Barcelona , 08193 Bellaterra, Spain.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase-peroxidase
A, B
728Burkholderia pseudomallei 1710bMutation(s): 1 
Gene Names: katGBURPS1710b_3366
EC: 1.11.1.21
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JNW6
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
 Ligand Interaction
NIZ
Query on NIZ

Download CCD File 
A, B
pyridine-4-carbohydrazide
C6 H7 N3 O
QRXWMOHMRWLFEY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
OXY
Query on OXY

Download CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.147 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.77α = 90
b = 115.59β = 90
c = 174.57γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-11 
  • Released Date: 2016-09-07 
  • Deposition Author(s): Loewen, P.C.
  • This entry supersedes: 4KA6

Funding OrganizationLocationGrant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)CanadaD9600

Revision History 

  • Version 1.0: 2016-09-07
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Derived calculations, Structure summary
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence