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Crystal structure of a COG4313 outer membrane channel.

van den Berg B, Bhamidimarri SP, Winterhalter M - Sci Rep (2015)

Bottom Line: Structure-function studies of this protein family have so far been hampered by a lack of structural information.Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules.Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.

ABSTRACT
COG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function studies of this protein family have so far been hampered by a lack of structural information. Here we present the X-ray crystal structure of Pput2725 from the biodegrader Pseudomonas putida F1, a COG4313 channel of unknown function, using data to 2.3 Å resolution. The structure shows a 12-stranded barrel with an N-terminal segment preceding the first β-strand occluding the lumen of the barrel. Single channel electrophysiology and liposome swelling experiments suggest that while the narrow channel visible in the crystal structure does allow passage of ions and certain small molecules in vitro, Pput2725 is unlikely to function as a channel for hydrophilic molecules. Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules. Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell. Our results provide the basis for structure-function studies of COG4313 family members with known function, such as the SphA sphingosine uptake channel of Pseudomonas aeruginosa.

No MeSH data available.


Related in: MedlinePlus

Comparison between Pput2725 and the toluene channel TodX.(A) Cut-away cartoon models viewed from the side, showing the barrel-occluding N-terminal domains. (B) Internal surfaces of the channels. The hydrophobic part of the OM is shown as a grey bar of ~25 Å wide (C). Surface views from the side, with residues in the Pput2725 lateral patch and on both sides of the TodX lateral opening colored green. The hydrophobic part of the OM (M) is delineated by horizontal lines. In all panels, Pput2725 and TodX are drawn to scale. (D) Possible models for substrate transport by COG4313 channels. Transport may occur either via a “classical” channel through the N-terminal domain into the periplasmic space (left), or via a lateral opening into the OM (right).
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f7: Comparison between Pput2725 and the toluene channel TodX.(A) Cut-away cartoon models viewed from the side, showing the barrel-occluding N-terminal domains. (B) Internal surfaces of the channels. The hydrophobic part of the OM is shown as a grey bar of ~25 Å wide (C). Surface views from the side, with residues in the Pput2725 lateral patch and on both sides of the TodX lateral opening colored green. The hydrophobic part of the OM (M) is delineated by horizontal lines. In all panels, Pput2725 and TodX are drawn to scale. (D) Possible models for substrate transport by COG4313 channels. Transport may occur either via a “classical” channel through the N-terminal domain into the periplasmic space (left), or via a lateral opening into the OM (right).

Mentions: The likely non-polar nature of the transported substrates and the presence of an N-terminal domain occluding the barrel warrant a comparison of COG4313 proteins with members of the FadL family, in particular those involved in transport of mono-aromatic hydrocarbons (MAH) such as the PpF1 toluene channel TodX9. Due to the larger size of TodX (420 residues), its occluding N-terminal domain is considerably larger (~40 residues) compared to that in Pput2725 (Fig. 7A). Despite this difference both proteins may have a classical channel through the N-terminal domain (Fig. 7B), raising the possibility that moderately hydrophobic transport substrates gain access to the periplasmic space via this channel. The presence of a bound detergent molecule in the Pput2725 channel (Fig. 4; det2) provides some support for such a “classical” transport mechanism.


Crystal structure of a COG4313 outer membrane channel.

van den Berg B, Bhamidimarri SP, Winterhalter M - Sci Rep (2015)

Comparison between Pput2725 and the toluene channel TodX.(A) Cut-away cartoon models viewed from the side, showing the barrel-occluding N-terminal domains. (B) Internal surfaces of the channels. The hydrophobic part of the OM is shown as a grey bar of ~25 Å wide (C). Surface views from the side, with residues in the Pput2725 lateral patch and on both sides of the TodX lateral opening colored green. The hydrophobic part of the OM (M) is delineated by horizontal lines. In all panels, Pput2725 and TodX are drawn to scale. (D) Possible models for substrate transport by COG4313 channels. Transport may occur either via a “classical” channel through the N-terminal domain into the periplasmic space (left), or via a lateral opening into the OM (right).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493636&req=5

f7: Comparison between Pput2725 and the toluene channel TodX.(A) Cut-away cartoon models viewed from the side, showing the barrel-occluding N-terminal domains. (B) Internal surfaces of the channels. The hydrophobic part of the OM is shown as a grey bar of ~25 Å wide (C). Surface views from the side, with residues in the Pput2725 lateral patch and on both sides of the TodX lateral opening colored green. The hydrophobic part of the OM (M) is delineated by horizontal lines. In all panels, Pput2725 and TodX are drawn to scale. (D) Possible models for substrate transport by COG4313 channels. Transport may occur either via a “classical” channel through the N-terminal domain into the periplasmic space (left), or via a lateral opening into the OM (right).
Mentions: The likely non-polar nature of the transported substrates and the presence of an N-terminal domain occluding the barrel warrant a comparison of COG4313 proteins with members of the FadL family, in particular those involved in transport of mono-aromatic hydrocarbons (MAH) such as the PpF1 toluene channel TodX9. Due to the larger size of TodX (420 residues), its occluding N-terminal domain is considerably larger (~40 residues) compared to that in Pput2725 (Fig. 7A). Despite this difference both proteins may have a classical channel through the N-terminal domain (Fig. 7B), raising the possibility that moderately hydrophobic transport substrates gain access to the periplasmic space via this channel. The presence of a bound detergent molecule in the Pput2725 channel (Fig. 4; det2) provides some support for such a “classical” transport mechanism.

Bottom Line: Structure-function studies of this protein family have so far been hampered by a lack of structural information.Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules.Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell.

View Article: PubMed Central - PubMed

Affiliation: Institute for Cell and Molecular Biosciences, The Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.

ABSTRACT
COG4313 proteins form a large and widespread family of outer membrane channels and have been implicated in the uptake of a variety of hydrophobic molecules. Structure-function studies of this protein family have so far been hampered by a lack of structural information. Here we present the X-ray crystal structure of Pput2725 from the biodegrader Pseudomonas putida F1, a COG4313 channel of unknown function, using data to 2.3 Å resolution. The structure shows a 12-stranded barrel with an N-terminal segment preceding the first β-strand occluding the lumen of the barrel. Single channel electrophysiology and liposome swelling experiments suggest that while the narrow channel visible in the crystal structure does allow passage of ions and certain small molecules in vitro, Pput2725 is unlikely to function as a channel for hydrophilic molecules. Instead, the presence of bound detergent molecules inside the barrel suggests that Pput2725 mediates uptake of hydrophobic molecules. Sequence alignments and the locations of highly conserved residues suggest the presence of a dynamic lateral opening through which hydrophobic molecules might gain entry into the cell. Our results provide the basis for structure-function studies of COG4313 family members with known function, such as the SphA sphingosine uptake channel of Pseudomonas aeruginosa.

No MeSH data available.


Related in: MedlinePlus