6RD3

Crystal structure of the wild type OmpK36 from Klebsiella pneumonia


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

OmpK36-mediated Carbapenem resistance attenuates ST258 Klebsiella pneumoniae in vivo.

Wong, J.L.C.Romano, M.Kerry, L.E.Kwong, H.S.Low, W.W.Brett, S.J.Clements, A.Beis, K.Frankel, G.

(2019) Nat Commun 10: 3957-3957

  • DOI: 10.1038/s41467-019-11756-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Carbapenem-resistance in Klebsiella pneumoniae (KP) sequence type ST258 is mediated by carbapenemases (e.g. KPC-2) and loss or modification of the major non-selective porins OmpK35 and OmpK36. However, the mechanism underpinning OmpK36-mediated resis ...

    Carbapenem-resistance in Klebsiella pneumoniae (KP) sequence type ST258 is mediated by carbapenemases (e.g. KPC-2) and loss or modification of the major non-selective porins OmpK35 and OmpK36. However, the mechanism underpinning OmpK36-mediated resistance and consequences of these changes on pathogenicity remain unknown. By solving the crystal structure of a clinical ST258 OmpK36 variant we provide direct structural evidence of pore constriction, mediated by a di-amino acid (Gly115-Asp116) insertion into loop 3, restricting diffusion of both nutrients (e.g. lactose) and Carbapenems. In the presence of KPC-2 this results in a 16-fold increase in MIC to Meropenem. Additionally, the Gly-Asp insertion impairs bacterial growth in lactose-containing medium and confers a significant in vivo fitness cost in a murine model of ventilator-associated pneumonia. Our data suggests that the continuous selective pressure imposed by widespread Carbapenem utilisation in hospital settings drives the expansion of KP expressing Gly-Asp insertion mutants, despite an associated fitness cost.


    Organizational Affiliation

    Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK. g.frankel@imperial.ac.uk.,Department of Surgery and Cancer, Section of Anaesthetics, Pain Medicine and Intensive Care, Imperial College London, London, UK.,Department of Life Sciences, Imperial College London, London, UK.,Department of Life Sciences, Imperial College London, London, UK. g.frankel@imperial.ac.uk.,Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, Oxfordshire, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OmpK36
A, B, C, D, E, F
345Klebsiella pneumoniaeMutation(s): 0 
Gene Names: ompK36
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpK36 osmoporin
Find proteins for D6QLY0 (Klebsiella pneumoniae)
Go to UniProtKB:  D6QLY0
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

Download SDF File 
Download CCD File 
A, B, C, D, E, F
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, B, C, D, E, F
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.194 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.090α = 90.00
b = 316.090β = 102.86
c = 73.790γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-09-11
    Type: Initial release