4D5B

Crystal structure of CymA from Klebsiella oxytoca

Summary for 4D5B

• Entry DOI: 10.2210/pdb4d5b/pdb
• Related: 4D51 4D5D
• Related PRD ID: PRD_900015
• Descriptor: CYMA, Cyclohexakis-(1-4)-(alpha-D-glucopyranose), (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE, ... (4 entities in total)
• Functional Keywords: transport protein, outer membrane channel, cyclodextrin transport, beta barrel
• Biological source: KLEBSIELLA OXYTOCA
• Total number of polymer chains: 2
• Total formula weight: 92967.85

Authors

van den Berg, B.,Bhamidimarri, S.P.,Kleinekathoefer, U.,Winterhalter, M. (deposition date: 2014-11-03, release date: 2015-06-03, Last modification date: 2023-12-20)

Primary citation

van den Berg, B.,Prathyusha Bhamidimarri, S.,Dahyabhai Prajapati, J.,Kleinekathofer, U.,Winterhalter, M.
Outer-membrane translocation of bulky small molecules by passive diffusion.
Proc. Natl. Acad. Sci. U.S.A., 112:E2991-E2999, 2015

PubMed Abstract: 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 ∼ 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 ∼ 15 Å. Here we show, by using X-ray crystallography, molecular dynamics simulations, and single-channel electrophysiology, that CymA forms a monomeric 14-stranded β-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.

PubMed: 26015567
DOI: 10.1073/pnas.1424835112

Experimental method

X-RAY DIFFRACTION (1.702 Å)