5SYJ

Crystal structure of the D141A variant of B. pseudomallei KatGin complex with isoniazid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/jp4123425
  • Primary Citation of Related Structures:  
    5SYI, 5SYJ

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase-peroxidase
A, B
728Burkholderia pseudomallei 1710bMutation(s): 1 
Gene Names: katGBURPS1710b_3366
EC: 1.11.1.21
UniProt
Find proteins for Q3JNW6 (Burkholderia pseudomallei (strain 1710b))
Explore Q3JNW6 
Go to UniProtKB:  Q3JNW6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3JNW6
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM
Query on HEM

Download Ideal Coordinates CCD File 
C [auth A],
M [auth B]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
NIZ
Query on NIZ

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K [auth A],
L [auth A],
U [auth B],
V [auth B]
pyridine-4-carbohydrazide
C6 H7 N3 O
QRXWMOHMRWLFEY-UHFFFAOYSA-N
MPD
Query on MPD

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
J [auth A]
P [auth B]
F [auth A],
G [auth A],
H [auth A],
J [auth A],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
I [auth A],
T [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CL
Query on CL

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E [auth A],
O [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
N [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.88 Å
  • R-Value Free: 0.170 
  • R-Value Work: 0.140 
  • R-Value Observed: 0.142 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 100.64α = 90
b = 114.64β = 90
c = 174.99γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2016-09-21 
  • Deposition Author(s): Loewen, P.C.
  • This entry supersedes: 4KWQ

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

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-21
    Type: Initial release
  • Version 1.1: 2017-09-27
    Changes: Author supporting evidence, Data collection, Derived calculations, Structure summary
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description