4ZRZ

PlyCB mutant R66E


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

A bacteriophage endolysin that eliminates intracellular streptococci.

Shen, Y.Barros, M.Vennemann, T.Gallagher, D.T.Yin, Y.Linden, S.B.Heselpoth, R.D.Spencer, D.J.Donovan, D.M.Moult, J.Fischetti, V.A.Heinrich, F.Losche, M.Nelson, D.C.

(2016) Elife 5

  • DOI: https://doi.org/10.7554/eLife.13152
  • Primary Citation of Related Structures:  
    4ZRZ

  • PubMed Abstract: 

    PlyC, a bacteriophage-encoded endolysin, lyses Streptococcus pyogenes (Spy) on contact. Here, we demonstrate that PlyC is a potent agent for controlling intracellular Spy that often underlies refractory infections. We show that the PlyC holoenzyme, mediated by its PlyCB subunit, crosses epithelial cell membranes and clears intracellular Spy in a dose-dependent manner. Quantitative studies using model membranes establish that PlyCB interacts strongly with phosphatidylserine (PS), whereas its interaction with other lipids is weak, suggesting specificity for PS as its cellular receptor. Neutron reflection further substantiates that PlyC penetrates bilayers above a PS threshold concentration. Crystallography and docking studies identify key residues that mediate PlyCB-PS interactions, which are validated by site-directed mutagenesis. This is the first report that a native endolysin can traverse epithelial membranes, thus substantiating the potential of PlyC as an antimicrobial for Spy in the extracellular and intracellular milieu and as a scaffold for engineering other functionalities.


  • Organizational Affiliation

    Institute for Bioscience and Biotechnology Research, University of Maryland, College Park, Rockville, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
PlyCB
A, B
71Fischettivirus C1Mutation(s): 1 
Gene Names: orf9
UniProt
Find proteins for Q7Y3F3 (Streptococcus phage C1)
Explore Q7Y3F3 
Go to UniProtKB:  Q7Y3F3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Y3F3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 
  • Space Group: I 4 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.428α = 90
b = 130.428β = 90
c = 130.428γ = 90
Software Package:
Software NamePurpose
d*TREKdata reduction
d*TREKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-09-14
    Type: Initial release
  • Version 1.1: 2017-03-22
    Changes: Data collection, Source and taxonomy
  • Version 1.2: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.3: 2023-09-27
    Changes: Data collection, Database references, Refinement description