4D5D: Crystal structure of CymA from Klebsiella oxytoca

The outer membrane (OM) of gram-negative bacteria forms a protective layer around the cell that serves as a permeability barrier to prevent unrestricted access of noxious substances. The permeability barrier of the OM results partly from the limited pore diameters of OM diffusion channels. As a consequence, there is an "OM size-exclusion limit," and the uptake of bulky molecules with molecular masses of more than approximately 600 Da is thought to be mediated by TonB-dependent, active transporters. Intriguingly, the OM protein CymA from Klebsiella oxytoca does not depend on TonB but nevertheless mediates efficient OM passage of cyclodextrins with diameters of up to approximately 15 A. Here we show, by using X-ray crystallography, molecular dynamics simulations, and single-channel electrophysiology, that CymA forms a monomeric 14-stranded beta-barrel with a large pore that is occluded on the periplasmic side by the N-terminal 15 residues of the protein. Representing a previously unidentified paradigm in OM transport, CymA mediates the passive diffusion of bulky molecules via an elegant transport mechanism in which a mobile element formed by the N terminus acts as a ligand-expelled gate to preserve the permeability barrier of the OM.
PDB ID: 4D5DDownload
MMDB ID: 129686
PDB Deposition Date: 2014/11/3
Updated in MMDB: 2015/06
Experimental Method:
x-ray diffraction
Resolution: 1.902  Å
Source Organism:
Similar Structures:
Biological Unit for 4D5D: dimeric; determined by author and by software (PISA)
Molecular Components in 4D5D
Label Count Molecule
Proteins (2 molecules)
Molecule annotation
Chemicals (24 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB