5L05

Crystal structure of catalase-peroxidase KATG of burkholderia pseudomallei treated with INH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 

wwPDB Validation 3D Report Full Report


This is version 2.0 of the entry. See complete history

Literature

Catalase-peroxidase KatG of Burkholderia pseudomallei at 1.7A resolution.

Carpena, X.Loprasert, S.Mongkolsuk, S.Switala, J.Loewen, P.C.Fita, I.

(2003) J. Mol. Biol. 327: 475-489

  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The catalase-peroxidase encoded by katG of Burkholderia pseudomallei (BpKatG) is 65% identical with KatG of Mycobacterium tuberculosis, the enzyme responsible for the activation of isoniazid as an antibiotic. The structure of a complex of BpKatG with ...

    The catalase-peroxidase encoded by katG of Burkholderia pseudomallei (BpKatG) is 65% identical with KatG of Mycobacterium tuberculosis, the enzyme responsible for the activation of isoniazid as an antibiotic. The structure of a complex of BpKatG with an unidentified ligand, has been solved and refined at 1.7A resolution using X-ray synchrotron data collected from crystals flash-cooled with liquid nitrogen. The crystallographic agreement factors R and R(free) are 15.3% and 18.6%, respectively. The crystallized enzyme is a dimer with one modified heme group and one metal ion, likely sodium, per subunit. The modification on the heme group involves the covalent addition of two or three atoms, likely a perhydroxy group, to the secondary carbon atom of the vinyl group on ring I. The added group can form hydrogen bonds with two water molecules that are also in contact with the active-site residues Trp111 and His112, suggesting that the modification may have a catalytic role. The heme modification is in close proximity to an unusual covalent adduct among the side-chains of Trp111, Tyr238 and Met264. In addition, Trp111 appears to be oxidized on C(delta1) of the indole ring. The main channel, providing access of substrate hydrogen peroxide to the heme, contains a region of unassigned electron density consistent with the binding of a pyridine nucleotide-like molecule. An interior cavity, containing the sodium ion and an additional region of unassigned density, is evident adjacent to the adduct and is accessible to the outside through a second funnel-shaped channel. A large cleft in the side of the subunit is evident and may be a potential substrate-binding site with a clear pathway for electron transfer to the active-site heme group through the adduct.


    Organizational Affiliation

    CID-CSIC, Jordi-Girona 18-26, 08034 Barcelona, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase-peroxidase
A, B
728Burkholderia pseudomallei (strain 1710b)Mutation(s): 0 
Gene Names: katG
EC: 1.11.1.21
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Go to UniProtKB:  Q3JNW6
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OXY
Query on OXY

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

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
HP5
Query on HP5

Download SDF File 
Download CCD File 
A, B
Peroxidized Heme Form 2
C34 H32 Fe N4 O6
NXBKHEUPFTWXKQ-FPZTWHSASA-L
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.176 
  • R-Value Work: 0.145 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 100.940α = 90.00
b = 115.620β = 90.00
c = 175.200γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-07-26 
  • Released Date: 2016-08-24 
  • Deposition Author(s): Loewen, P.C.
  • This entry supersedes: 1MWV

Revision History 

  • Version 1.0: 2016-08-24
    Type: Initial release
  • Version 1.1: 2017-11-22
    Type: Data collection, Derived calculations, Refinement description, Structure summary
  • Version 2.0: 2018-03-28
    Type: Atomic model, Data collection, Derived calculations, Refinement description