9PME | pdb_00009pme

Crystallographic structure of MazF-E24A toxin bound to SamF


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 
    0.203 (Depositor), 0.202 (DCC) 
  • R-Value Work: 
    0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 
    0.171 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Development of a Potent and Functional In Vivo Peptide Competitive Inhibitor for the Toxin MazF.

Pizzolato-Cezar, L.R.Vitale, P.M.Liria, C.W.Pineda, M.A.R.Lacerda, C.D.Marana, S.R.Nascimento, A.F.Z.Sassonia, R.C.Sgro, G.G.Salinas, R.K.Machini, M.T.

(2025) J Med Chem 68: 21665-21682

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c02001
  • Primary Citation of Related Structures:  
    9PME

  • PubMed Abstract: 

    Cell growth regulation granted by toxin-antitoxin systems enables bacteria to fight phage infections, evade host immune defenses, and survive antibiotic treatment. In this work, a potent and specific peptide competitive inhibitor for the Escherichia coli toxin MazF was developed and named Small Antitoxin of MazF (SamF). Employing a set of N -acetylated and C -amidated synthetic peptides, biophysical methods, biochemistry, and molecular biology techniques, we demonstrated that SamF binds tightly and with high specificity to MazF in vitro and in vivo , blocking access to the substrate binding site. Coexpression of SamF with MazF in E. coli efficiently counteracted the metabolic downregulation imposed by the toxin and the formation of antibiotic persisters. Altogether, our data uncovered a new MazF druggable site and an excellent scaffold for the design of antimicrobials. SamF is also a promising tool to study MazF in vitro and its physiological function in bacteria.


  • Organizational Affiliation
    • Department of Biochemistry, Institute of Chemistry, University of São Paulo, Av. Prof. Lineu Prestes 748, 05508-000 São Paulo SP, Brazil.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Endoribonuclease toxin MazF111Escherichia coli K-12Mutation(s): 1 
Gene Names: mazFchpAchpAKb2782JW2753
EC: 3.1.27
UniProt
Find proteins for P0AE70 (Escherichia coli (strain K12))
Explore P0AE70 
Go to UniProtKB:  P0AE70
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0AE70
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
peptide SER-HIS-LEU-PHE-TRP-ALA-GLN-PHE-ASP-GLU-TYR-PHE14synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free:  0.203 (Depositor), 0.202 (DCC) 
  • R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
  • R-Value Observed: 0.171 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.222α = 90
b = 59.222β = 90
c = 66.432γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Sao Paulo Research Foundation (FAPESP)Brazil2021/10577-0
Sao Paulo Research Foundation (FAPESP)Brazil2022/01825-2

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release
  • Version 1.1: 2025-11-05
    Changes: Database references, Source and taxonomy