9HTU | pdb_00009htu

Structure of endolysin PlyP100 catalytic domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.183 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.152 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 
    0.153 (Depositor) 

Starting Model: experimental
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Literature

Structural and functional insights into Listeriamonocytogenes phage endolysin PlyP100: A promising food safety tool.

Bateman, K.R.Scaletti Hutchinson, E.Widmalm, G.Miller, M.J.Stenmark, P.

(2025) J Biological Chem 301: 110295-110295

  • DOI: https://doi.org/10.1016/j.jbc.2025.110295
  • Primary Citation of Related Structures:  
    9HTU

  • PubMed Abstract: 

    Listeria monocytogenes is a ubiquitous, psychrotrophic human pathogen that can cause listeriosis, a serious illness for vulnerable populations. Some foods, such as Hispanic-style fresh cheeses like queso fresco, pose a specific risk because there are no widely accepted or available methods for L. monocytogenes mitigation that are both effective and able to maintain the properties of the products. Listeria-specific bacteriophages encode endolysins that can cleave the peptidoglycan layer of L. monocytogenes cells externally, showing promise as a potential solution to this problem. PlyP100, from the GRAS Listeria phage P100, is one such endolysin that can prevent the growth of L. monocytogenes in both lab culture conditions and a miniaturized queso fresco model. In this work, we aimed to understand the structural and functional properties of PlyP100. An AlphaFold prediction suggested the presence of three separate domains (D1, D2, and D3). By solving the crystal structure of D1 and assessing various domain truncations, we present evidence that D1 is responsible for catalytic activity, D3 is sufficient for cell wall binding, and D2 is necessary for full function of the enzyme against live cells. Additionally, we performed point mutations in D1 and compared PlyP100 to proteins with similar structures, including Streptococcus pneumoniae LytA and Listeria endolysin Ply511, to understand its specific enzymatic mechanism and target strain specificity. These insights into the structure and function of PlyP100 will aid future work aiming to engineer better endolysins as safe food antimicrobials.


  • Organizational Affiliation
    • Department of Food Science and Human Nutrition, University of Illinois Urbana-Champaign, Urbana, Illinois, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
N-acetylmuramoyl-L-alanine amidase180Listeria phage LP-125Mutation(s): 0 
Gene Names: LP125_088
UniProt
Find proteins for S4U9Y8 (Listeria phage LP-125)
Explore S4U9Y8 
Go to UniProtKB:  S4U9Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupS4U9Y8
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.183 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.152 (Depositor), 0.164 (DCC) 
  • R-Value Observed: 0.153 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.306α = 90
b = 65.864β = 90
c = 96.512γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swedish Research CouncilSweden--

Revision History  (Full details and data files)

  • Version 1.0: 2025-06-25
    Type: Initial release
  • Version 1.1: 2025-07-02
    Changes: Database references