4C50

Crystal Structure of the Catalase-Peroxidase (KatG) D137S mutant from Mycobacterium Tuberculosis

• PDB DOI: https://doi.org/10.2210/pdb4C50/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Mycobacterium tuberculosis H37Rv
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-09-10 Released: 2013-11-13 
• Deposition Author(s): Hersleth, H.-P., Zhao, X., Magliozzo, R.S., Andersson, K.K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.311 
• R-Value Work: 0.264 
• R-Value Observed: 0.266 

Starting Model: experimental

Literature

Access Channel Residues Ser315 and Asp137 in Mycobacterium Tuberculosis Catalase-Peroxidase (Katg) Control Peroxidatic Activation of the Pro-Drug Isoniazid.

Zhao, X., Hersleth, H.P., Zhu, J., Andersson, K.K., Magliozzo, R.S.

(2013) Chem Commun (Camb) 49: 11650

• PubMed: 24185282 
• DOI: https://doi.org/10.1039/c3cc47022a
• Primary Citation of Related Structures:  
  4C50, 4C51


• PubMed Abstract: 
  

  Peroxidatic activation of the anti-tuberculosis pro-drug isoniazid by Mycobacterium tuberculosis catalase-peroxidase (KatG) is regulated by gating residues of a heme access channel. The steric restriction at the bottleneck of this channel is alleviated by replacement of residue Asp137 with Ser, according to crystallographic and kinetic studies.

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Organizational Affiliation: 

Department of Chemistry, Brooklyn College and The Graduate Center of The City University of New York, 2900 Bedford Avenue, Brooklyn, NY 11210, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 162.79 kDa 
• Atom Count: 11,241 
• Modelled Residue Count: 1,432 
• Deposited Residue Count: 1,480 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CATALASE-PEROXIDASE	A, B	740	Mycobacterium tuberculosis H37Rv	Mutation(s): 1  EC: 1.11.1.21
UniProt
Find proteins for P9WIE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)) Explore P9WIE5  Go to UniProtKB:  P9WIE5

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	D [auth A], F [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
GLC	C [auth A]	alpha-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-DVKNGEFBSA-N
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.311 
• R-Value Work: 0.264 
• R-Value Observed: 0.266 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.59	α = 90
b = 150.59	β = 90
c = 157.35	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-13 
Deposition Author(s): Hersleth, H.-P., Zhao, X., Magliozzo, R.S., Andersson, K.K.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2013-11-27
  Changes: Database references
• Version 1.2: 2019-10-30
  Changes: Advisory, Data collection, Derived calculations, Other
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary