9GY1 | pdb_00009gy1

High resolution crystal structure of StM23 peptidoglycan hydrolase

• PDB DOI: https://doi.org/10.2210/pdb9GY1/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus thermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-10-01 Released: 2025-06-04 
• Deposition Author(s): Kaus-Drobek, M., Nowacka, M.
• Funding Organization(s): National Center for Research and Development (Poland)

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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

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

• PubMed: 40325189 
• DOI: https://doi.org/10.1038/s41598-025-99141-2
• Primary Citation 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.

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Organizational Affiliation: 
• Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland. [e-mail].
Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland.
Electron Microscopy Research Unit, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland.
Nofima, Norwegian Institute for Food, Fisheries and Aquaculture Research, P.O. Box 210, 1431, Ås, Norway.
Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
Preclinical Drug Development Facility, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109, Warsaw, Poland.
Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Pawinskiego 5, 02-106, Warsaw, Poland. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.65 kDa 
• Atom Count: 1,206 
• Modeled Residue Count: 133 
• Deposited Residue Count: 144 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidase, M23 family	A	144	Streptococcus thermophilus	Mutation(s): 0  Gene Names: HMPREF0291_12130
UniProt
Find proteins for D7WEP7 (Corynebacterium genitalium ATCC 33030) Explore D7WEP7  Go to UniProtKB:  D7WEP7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	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 = 52.69	α = 90
b = 52.69	β = 90
c = 77.49	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-06-04 
Deposition Author(s): Kaus-Drobek, M., Nowacka, M.

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Funding Organization	Location	Grant Number
National Center for Research and Development (Poland)	Poland	NOR/POLNOR/PrevEco/0021/2019

Revision History  

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