8Q2G

X-ray structure of LysECD7 endolysin against Gram-negative bacteria


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.268 

Starting Model: experimental
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Literature

Development of novel antimicrobials with engineered endolysin LysECD7-SMAP to combat Gram-negative bacterial infections.

Vasina, D.V.Antonova, N.P.Gushchin, V.A.Aleshkin, A.V.Fursov, M.V.Fursova, A.D.Gancheva, P.G.Grigoriev, I.V.Grinkevich, P.Kondratev, A.V.Kostarnoy, A.V.Lendel, A.M.Makarov, V.V.Nikiforova, M.A.Pochtovyi, A.A.Prudnikova, T.Remizov, T.A.Shevlyagina, N.V.Siniavin, A.E.Smirnova, N.S.Terechov, A.A.Tkachuk, A.P.Usachev, E.V.Vorobev, A.M.Yakimakha, V.S.Yudin, S.M.Zackharova, A.A.Zhukhovitsky, V.G.Logunov, D.Y.Gintsburg, A.L.

(2024) J Biomed Sci 31: 75-75

  • DOI: https://doi.org/10.1186/s12929-024-01065-y
  • Primary Citation of Related Structures:  
    8Q2G

  • PubMed Abstract: 

    Among the non-traditional antibacterial agents in development, only a few targets critical Gram-negative bacteria such as carbapenem-resistant Pseudomonas aeruginosa, Acinetobacter baumannii or cephalosporin-resistant Enterobacteriaceae. Endolysins and their genetically modified versions meet the World Health Organization criteria for innovation, have a novel mode of antibacterial action, no known bacterial cross-resistance, and are being intensively studied for application against Gram-negative pathogens. The study presents a multidisciplinary approach, including genetic engineering of LysECD7-SMAP and production of recombinant endolysin, its analysis by crystal structure solution following molecular dynamics simulations and evaluation of antibacterial properties. Two types of antimicrobial dosage forms were formulated, resulting in lyophilized powder for injection and hydroxyethylcellulose gel for topical administration. Their efficacy was estimated in the treatment of sepsis, and pneumonia models in BALB/c mice, diabetes-associated wound infection in the leptin receptor-deficient db/db mice and infected burn wounds in rats. In this work, we investigate the application strategies of the engineered endolysin LysECD7-SMAP and its dosage forms evaluated in preclinical studies. The catalytic domain of the enzyme shares the conserved structure of endopeptidases containing a putative antimicrobial peptide at the C-terminus of polypeptide chain. The activity of endolysins has been demonstrated against a range of pathogens, such as Klebsiella pneumoniae, A. baumannii, P. aeruginosa, Staphylococcus haemolyticus, Achromobacter spp, Burkholderia cepacia complex and Haemophylus influenzae, including those with multidrug resistance. The efficacy of candidate dosage forms has been confirmed in in vivo studies. Some aspects of the interaction of LysECD7-SMAP with cell wall molecular targets are also discussed. Our studies demonstrate the potential of LysECD7-SMAP therapeutics for the systemic or topical treatment of infectious diseases caused by susceptible Gram-negative bacterial species and are critical to proceed LysECD7-SMAP-based antimicrobials trials to advanced stages.


  • Organizational Affiliation

    N.F. Gamaleya National Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia. d.v.vasina@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidoglycan L-alanyl-D-glutamate endopeptidase139Escherichia phage ECD7Mutation(s): 0 
Gene Names: cwlK
UniProt
Find proteins for A0A220NTE5 (Escherichia phage ECD7)
Explore A0A220NTE5 
Go to UniProtKB:  A0A220NTE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A220NTE5
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.49 Å
  • R-Value Free: 0.358 
  • R-Value Work: 0.268 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.568α = 90
b = 82.334β = 90
c = 64.604γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
Arcimboldophasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-07-31
    Type: Initial release
  • Version 1.1: 2024-08-07
    Changes: Database references