The crystal structure of an engineered phage lysin containing the binding domain of pesticin and the killing domain of T4-lysozyme

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Structural engineering of a phage lysin that targets Gram-negative pathogens.

Lukacik, P.Barnard, T.J.Keller, P.W.Chaturvedi, K.S.Seddiki, N.Fairman, J.W.Noinaj, N.Kirby, T.L.Henderson, J.P.Steven, A.C.Hinnebusch, B.J.Buchanan, S.K.

(2012) Proc Natl Acad Sci U S A 109: 9857-9862

  • DOI: https://doi.org/10.1073/pnas.1203472109
  • Primary Citation of Related Structures:  
    4EPA, 4EPF, 4EPI, 4EXM

  • PubMed Abstract: 

    Bacterial pathogens are becoming increasingly resistant to antibiotics. As an alternative therapeutic strategy, phage therapy reagents containing purified viral lysins have been developed against gram-positive organisms but not against gram-negative organisms due to the inability of these types of drugs to cross the bacterial outer membrane. We solved the crystal structures of a Yersinia pestis outer membrane transporter called FyuA and a bacterial toxin called pesticin that targets this transporter. FyuA is a β-barrel membrane protein belonging to the family of TonB dependent transporters, whereas pesticin is a soluble protein with two domains, one that binds to FyuA and another that is structurally similar to phage T4 lysozyme. The structure of pesticin allowed us to design a phage therapy reagent comprised of the FyuA binding domain of pesticin fused to the N-terminus of T4 lysozyme. This hybrid toxin kills specific Yersinia and pathogenic E. coli strains and, importantly, can evade the pesticin immunity protein (Pim) giving it a distinct advantage over pesticin. Furthermore, because FyuA is required for virulence and is more common in pathogenic bacteria, the hybrid toxin also has the advantage of targeting primarily disease-causing bacteria rather than indiscriminately eliminating natural gut flora.

  • Organizational Affiliation

    Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pesticin, Lysozyme Chimera
A, B, C, D
347Yersinia pestisTequatrovirus T4
This entity is chimeric
Mutation(s): 4 
Gene Names: pstYP_pPCP06YPPCP1.05cE
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for Q57159 (Yersinia pestis)
Explore Q57159 
Go to UniProtKB:  Q57159
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720Q57159
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 108.427α = 90
b = 108.427β = 90
c = 109.752γ = 120
Software Package:
Software NamePurpose
SERGUIdata collection
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2012-07-04
    Changes: Database references
  • Version 1.2: 2017-07-26
    Changes: Refinement description, Source and taxonomy
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Refinement description