5SXX

Crystal structure of the E198A variant of Burkholderia pseudomallei catalase-peroxidase KatG with INH

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Isonicotinic acid hydrazide conversion to Isonicotinyl-NAD by catalase-peroxidases.

Wiseman, B., Carpena, X., Feliz, M., Donald, L.J., Pons, M., Fita, I., Loewen, P.C.

(2010) J Biol Chem 285: 26662-26673

  • DOI: 10.1074/jbc.M110.139428
  • Primary Citation of Related Structures:  
    5SXS, 5SXR, 5SXT, 5SXW, 5SXX, 5SXQ

  • PubMed Abstract: 

    • Activation of the pro-drug isoniazid (INH) as an anti-tubercular drug in Mycobacterium tuberculosis involves its conversion to isonicotinyl-NAD, a reaction that requires the catalase-peroxidase KatG. This report shows that the reaction proceeds in th ...

    Activation of the pro-drug isoniazid (INH) as an anti-tubercular drug in Mycobacterium tuberculosis involves its conversion to isonicotinyl-NAD, a reaction that requires the catalase-peroxidase KatG. This report shows that the reaction proceeds in the absence of KatG at a slow rate in a mixture of INH, NAD(+), Mn(2+), and O(2), and that the inclusion of KatG increases the rate by >7 times. Superoxide, generated by either Mn(2+)- or KatG-catalyzed reduction of O(2), is an essential intermediate in the reaction. Elimination of the peroxidatic process by mutation slows the rate of reaction by 60% revealing that the peroxidatic process enhances, but is not essential for isonicotinyl-NAD formation. The isonicotinyl-NAD(*+) radical is identified as a reaction intermediate, and its reduction by superoxide is proposed. Binding sites for INH and its co-substrate, NAD(+), are identified for the first time in crystal complexes of Burkholderia pseudomallei catalase-peroxidase with INH and NAD(+) grown by co-crystallization. The best defined INH binding sites were identified, one in each subunit, on the opposite side of the protein from the entrance to the heme cavity in a funnel-shaped channel. The NAD(+) binding site is approximately 20 A from the entrance to the heme cavity and involves interactions primarily with the AMP portion of the molecule in agreement with the NMR saturation transfer difference results.

    Organizational Affiliation: 

    Department of Microbiology, University of Manitoba,Winnipeg, Manitoba, Canada.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Catalase-peroxidaseA, B728Burkholderia pseudomallei 1710bMutation(s): 1 
Gene Names: katG, BURPS1710b_3366
EC: 1.11.1.21
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JNW6 
Go to UniProtKB:  Q3JNW6
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM
Download Ideal Coordinates CCD File 
A, B
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L		 Ligand Interaction
MPD
Query on MPD
Download Ideal Coordinates CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
OXY
Query on OXY
Download Ideal Coordinates CCD File 
A, B
OXYGEN MOLECULE
O2
MYMOFIZGZYHOMD-UHFFFAOYSA-N		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates 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: 0.169 
  • R-Value Work: 0.142 
  • R-Value Observed: 0.143 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.57α = 90
b = 115.94β = 90
c = 174.73γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-10 
  • Released Date: 2016-09-07 
    • Deposition Author(s): Loewen, P.C.
  • This entry supersedes: 3N3S
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