8CZP

2.25 angstrom resolution crystal structure of as-isolated KatG from Mycobacterium tuberculosis with an MYW cofactor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Indole-N-Linked Hydroperoxyl Adduct of Protein-Derived Cofactor Modulating Catalase-Peroxidase Functions.

Li, J.Duan, R.Traore, E.S.Nguyen, R.C.Davis, I.Griffth, W.P.Goodwin, D.C.Jarzecki, A.A.Liu, A.

(2024) Angew Chem Int Ed Engl : e202407018-e202407018

  • DOI: https://doi.org/10.1002/anie.202407018
  • Primary Citation of Related Structures:  
    8CZP, 8U3P, 8W1W, 8W1X, 8W1Y

  • PubMed Abstract: 

    Bifunctional catalase-peroxidase (KatG) features a posttranslational methionine-tyrosine-tryptophan (MYW) crosslinked cofactor crucial for its catalase function, enabling pathogens to neutralize hydrogen peroxide during infection. We discovered the presence of indole nitrogen-linked hydroperoxyl adduct (MYW-OOH) in Mycobacterium tuberculosis KatG in the solution state under ambient conditions, suggesting its natural occurrence. By isolating predominantly MYW-OOH-containing KatG protein, we investigated the chemical stability and functional impact of MYW-OOH. We discovered that MYW-OOH inhibits catalase activity, presenting a unique temporary lock. Exposure to peroxide or increased temperature removes the hydroperoxyl adduct from the protein cofactor, converting MYW-OOH to MYW and restoring the detoxifying ability of the enzyme against hydrogen peroxide. Thus, the N-linked hydroperoxyl group is releasable. KatG with MYW-OOH represents a catalase dormant, but primed, state of the enzyme. These findings provide insight into chemical strategies targeting the bifunctional enzyme KatG in pathogens, highlighting the role of N-linked hydroperoxyl modifications in enzymatic function.


  • Organizational Affiliation

    University of Texas at San Antonio, Chemistry, UNITED STATES.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Catalase-peroxidase
A, B
741Mycobacterium tuberculosisMutation(s): 0 
Gene Names: katGERS007661_00994ERS024276_01596
EC: 1.11.1.21
UniProt
Find proteins for P9WIE5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WIE5 
Go to UniProtKB:  P9WIE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WIE5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.25 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.240 
  • R-Value Observed: 0.241 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.699α = 90
b = 150.699β = 90
c = 155.491γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data

  • Released Date: 2023-12-13 
  • Deposition Author(s): Li, J., Liu, A.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM108988

Revision History  (Full details and data files)

  • Version 1.0: 2023-12-13
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Database references, Structure summary