4E81

Crystal structure of the substrate binding domain of E.coli DnaK in complex with a short apidaecin peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Api88 is a novel antibacterial designer Peptide to treat systemic infections with multidrug-resistant gram-negative pathogens.

Czihal, P.Knappe, D.Fritsche, S.Zahn, M.Berthold, N.Piantavigna, S.Muller, U.Van Dorpe, S.Herth, N.Binas, A.Kohler, G.De Spiegeleer, B.Martin, L.L.Nolte, O.Strater, N.Alber, G.Hoffmann, R.

(2012) ACS Chem Biol 7: 1281-1291

  • DOI: https://doi.org/10.1021/cb300063v
  • Primary Citation of Related Structures:  
    4E81

  • PubMed Abstract: 

    The emergence of multiple-drug-resistant (MDR) bacterial pathogens in hospitals (nosocomial infections) presents a global threat of growing importance, especially for Gram-negative bacteria with extended spectrum β-lactamase (ESBL) or the novel New Delhi metallo-β-lactamase 1 (NDM-1) resistance. Starting from the antibacterial peptide apidaecin 1b, we have optimized the sequence to treat systemic infections with the most threatening human pathogens, such as Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. The lead compound Api88 enters bacteria without lytic effects at the membrane and inhibits chaperone DnaK at the substrate binding domain with a K(D) of 5 μmol/L. The Api88-DnaK crystal structure revealed that Api88 binds with a seven residue long sequence (PVYIPRP), in two different modes. Mice did not show any sign of toxicity when Api88 was injected four times intraperitoneally at a dose of 40 mg/kg body weight (BW) within 24 h, whereas three injections of 1.25 mg/kg BW and 5 mg/kg BW were sufficient to rescue all animals in lethal sepsis models using pathogenic E. coli strains ATCC 25922 and Neumann, respectively. Radioactive labeling showed that Api88 enters all organs investigated including the brain and is cleared through both the liver and kidneys at similar rates. In conclusion, Api88 is a novel, highly promising, 18-residue peptide lead compound with favorable in vitro and in vivo properties including a promising safety margin.


  • Organizational Affiliation

    Institute of Bioanalytical Chemistry, Faculty of Chemistry and Mineralogy, College of Veterinary Medicine, Universität Leipzig, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chaperone protein DnaK
A, B
219Escherichia coli K-12Mutation(s): 0 
Gene Names: b0014dnaKgroPgrpFJW0013seg
UniProt
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Explore P0A6Y8 
Go to UniProtKB:  P0A6Y8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A6Y8
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
apidaecin peptide fragment
C, D
10Apis melliferaMutation(s): 0 
UniProt
Find proteins for Q06602 (Apis mellifera)
Explore Q06602 
Go to UniProtKB:  Q06602
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ06602
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.777α = 90
b = 60.202β = 90
c = 67.453γ = 90
Software Package:
Software NamePurpose
MAR345data collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-01
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-02-28
    Changes: Data collection, Database references, Derived calculations