4PAE

Crystal structure of catalase-peroxidase (KatG) W78F mutant from Synechococcus elongatus PCC7942


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.206 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the catalase-peroxidase KatG W78F mutant from Synechococcus elongatus PCC7942 in complex with the antitubercular pro-drug isoniazid.

Kamachi, S.Hirabayashi, K.Tamoi, M.Shigeoka, S.Tada, T.Wada, K.

(2015) Febs Lett. 589: 131-137

  • DOI: 10.1016/j.febslet.2014.11.037
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Isoniazid (INH) is a pro-drug that has been extensively used to treat tuberculosis. INH is activated by the heme enzyme catalase-peroxidase (KatG), but the mechanism of the activation is poorly understood, in part because the INH binding site has not ...

    Isoniazid (INH) is a pro-drug that has been extensively used to treat tuberculosis. INH is activated by the heme enzyme catalase-peroxidase (KatG), but the mechanism of the activation is poorly understood, in part because the INH binding site has not been clearly established. Here, we observed that a single-residue mutation of KatG from Synechococcus elongatus PCC7942 (SeKatG), W78F, enhances INH activation. The crystal structure of INH-bound KatG-W78F revealed that INH binds to the heme pocket. The results of a thermal-shift assay implied that the flexibility of the SeKatG molecule is increased by the W78F mutation, allowing the INH molecule to easily invade the heme pocket through the access channel on the γ-edge side of the heme.


    Organizational Affiliation

    Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan. Electronic address: tada@b.s.osakafu-u.ac.jp.,Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan; Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan.,Faculty of Agriculture, Kinki University, Nakamachi, Nara 631-8505, Japan.,Organization for Promotion of Tenure Track, University of Miyazaki, Miyazaki 889-1692, Japan. Electronic address: keiwada@med.miyazaki-u.ac.jp.,Graduate School of Science, Osaka Prefecture University, Sakai, Osaka 599-8531, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Catalase-peroxidase
A
720Synechococcus elongatus (strain PCC 7942)Mutation(s): 1 
Gene Names: katG
EC: 1.11.1.21
Find proteins for Q31MN3 (Synechococcus elongatus (strain PCC 7942))
Go to UniProtKB:  Q31MN3
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
NIZ
Query on NIZ

Download SDF File 
Download CCD File 
A
pyridine-4-carbohydrazide
isonicotinic acid hydrazid
C6 H7 N3 O
QRXWMOHMRWLFEY-UHFFFAOYSA-N
 Ligand Interaction
HEB
Query on HEB

Download SDF File 
Download CCD File 
A
HEME B/C
HYBRID BETWEEN B AND C TYPE HEMES (PROTOPORPHYRIN IX CONTAINING FE)
C34 H34 Fe N4 O4
NEGHHAJBRZGUAY-ICENSXKYDL
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.206 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 107.673α = 90.00
b = 107.673β = 90.00
c = 204.788γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2017-11-01
    Type: Author supporting evidence, Data collection, Database references, Derived calculations, Other, Source and taxonomy