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: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/cb300063v

  • 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 D ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chaperone protein DnaK
A, B
219Escherichia coli (strain K12)Gene Names: dnaK (groP, grpF, seg)
Find proteins for P0A6Y8 (Escherichia coli (strain K12))
Go to UniProtKB:  P0A6Y8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
apidaecin peptide fragment
C, D
10Apis melliferaGene Names: APID73
Find proteins for Q06602 (Apis mellifera)
Go to UniProtKB:  Q06602
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 144.777α = 90.00
b = 60.202β = 90.00
c = 67.453γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
SCALAdata scaling
XDSdata reduction
REFMACrefinement
MAR345data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-03-19 
  • Released Date: 2012-05-30 
  • Deposition Author(s): Zahn, M., Straeter, N.

Revision History 

  • Version 1.0: 2012-05-30
    Type: Initial release
  • Version 1.1: 2012-08-01
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Refinement description