9GY1 | pdb_00009gy1

High resolution crystal structure of StM23 peptidoglycan hydrolase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free: 
    0.144 (Depositor), 0.144 (DCC) 
  • R-Value Work: 
    0.122 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 
    0.123 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

From discovery to potential application: engineering a novel M23 peptidase to combat Listeria monocytogenes.

Kaus-Drobek, M.Nowacka, M.Gewartowska, M.Korzeniowska Nee Wiweger, M.Jensen, M.R.Moretro, T.Heir, E.Nowak, E.Sabala, I.

(2025) Sci Rep 15: 15628-15628

  • DOI: https://doi.org/10.1038/s41598-025-99141-2
  • Primary Citation of Related Structures:  
    9GY1

  • PubMed Abstract: 

    Peptidoglycan hydrolases are promising alternatives for combating pathogens due to their specificity and potent bacteriolytic activity. In this study, a novel M23 peptidase from Streptococcus thermophilus NCTC10353, designated StM23, was discovered and characterized. It exhibited antibacterial activity against Listeria monocytogenes and other Gram-positive bacteria with meso-DAP-type peptidoglycan, including Bacillus subtilis and Bacillus cereus. To enhance StM23's efficacy and specificity, a chimeric enzyme, StM23_CWT, was engineered by fusing its catalytic domain with a cell wall-targeting domain (CWT) from SpM23B, a peptidoglycan hydrolase found in Staphylococcus pettenkoferi. The engineered chimera demonstrated expanded specificity, showing activity against Staphylococcus aureus and Enterococcus faecium. Its ability to disrupt L. monocytogenes cells was visualized by electron microscopy. The enzyme effectively disrupted biofilm structures and decontaminated surfaces like glass, stainless steel, and silicone, showcasing its industrial potential. Safety evaluations using zebrafish, moth larvae, and human cell models confirmed its non-toxic profile, supporting its broad applicability. Based on these findings, StM23_CWT is a novel and potent antimicrobial agent with significant potential to reduce the risk of listeriosis and control persistent pathogens.


  • Organizational Affiliation
    • Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland. mdrobek@imdik.pan.pl.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidase, M23 family144Streptococcus thermophilusMutation(s): 0 
Gene Names: HMPREF0291_12130
UniProt
Find proteins for D7WEP7 (Corynebacterium genitalium ATCC 33030)
Explore D7WEP7 
Go to UniProtKB:  D7WEP7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupD7WEP7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.35 Å
  • R-Value Free:  0.144 (Depositor), 0.144 (DCC) 
  • R-Value Work:  0.122 (Depositor), 0.122 (DCC) 
  • R-Value Observed: 0.123 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.69α = 90
b = 52.69β = 90
c = 77.49γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Center for Research and Development (Poland)PolandNOR/POLNOR/PrevEco/0021/2019

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-04
    Type: Initial release