SASDC33: Colicin N delta 1-39 (ColN N40)

Basic information

• Entry: Database: SASBDB / ID: SASDC33

Sample

Colicin N delta 1-39

• Colicin N delta 1-39 (protein), ColN N40, Escherichia coli

Function / homology

Function:

negative regulation of ion transmembrane transporter activity / pore-forming activity / killing of cells of another organism / defense response to Gram-negative bacterium / transmembrane transporter binding / plasma membrane

Domain/homology:

Channel forming colicin, C-terminal cytotoxic / Channel forming colicin, C-terminal domain superfamily / Colicin pore forming domain / Channel forming colicins signature.

Component:

Colicin-N

• Biological species: Escherichia coli (E. coli)
• Citation: Journal: Biophys J / Year: 2017; Title: The Two-State Prehensile Tail of the Antibacterial Toxin Colicin N.; Authors: Christopher L Johnson / Alexandra S Solovyova / Olli Hecht / Colin Macdonald / Helen Waller / J Günter Grossmann / Geoffrey R Moore / Jeremy H Lakey / ; Abstract: Intrinsically disordered regions within proteins are critical elements in many biomolecular interactions and signaling pathways. Antibacterial toxins of the colicin family, which could provide new antibiotic functions against resistant bacteria, contain disordered N-terminal translocation domains (T-domains) that are essential for receptor binding and the penetration of the Escherichia coli outer membrane. Here we investigate the conformational behavior of the T-domain of colicin N (ColN-T) to understand why such domains are widespread in toxins that target Gram-negative bacteria. Like some other intrinsically disordered proteins in the solution state of the protein, ColN-T shows dual recognition, initially interacting with other domains of the same colicin N molecule and later, during cell killing, binding to two different receptors, OmpF and TolA, in the target bacterium. ColN-T is invisible in the high-resolution x-ray model and yet accounts for 90 of the toxin's 387 amino acid residues. To reveal its solution structure that underlies such a dynamic and complex system, we carried out mutagenic, biochemical, hydrodynamic and structural studies using analytical ultracentrifugation, NMR, and small-angle x-ray scattering on full-length ColN and its fragments. The structure was accurately modeled from small-angle x-ray scattering data by treating ColN as a flexible system, namely by the ensemble optimization method, which enables a distribution of conformations to be included in the final model. The results reveal, to our knowledge, for the first time the dynamic structure of a colicin T-domain. ColN-T is in dynamic equilibrium between a compact form, showing specific self-recognition and resistance to proteolysis, and an extended form, which most likely allows for effective receptor binding.

Contact author

• Alex Solovyova (Newcastle University, Newcastle, UK)

Models

• Model #1203: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 0.455625 / P-value: 0.064000; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1204: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 0.455625 / P-value: 0.064000; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1205: ; Type: atomic / Radius of dummy atoms: 1.90 A / Chi-square value: 0.455625 / P-value: 0.064000; Search similar-shape structures of this assembly by Omokage search (details)
• Model #1206: ; Type: dummy / Radius of dummy atoms: 2.20 A / Chi-square value: 0.659344 / P-value: 0.372600; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Colicin N delta 1-39 / Specimen concentration: 0.50-7.50
• Buffer: Name: 50 mM Na-Phosphate 300 mM NaCl / pH: 7.6

Entity #625

Name: ColN N40 / Type: protein / Description: Colicin N delta 1-39 / Formula weight: 39.212 / Num. of mol.: 1 / Source: Escherichia coli / References: UniProt: P08083
Sequence:

MSNGWSWSNK PHKNDGFHSD GSYHITFHGD NNSKPKPGGN SGNRGNNGDG ASAKVGEITI TPDNSKPGRY ISSNPEYSLL AKLIDAESIK GTEVYTFHTR KGQYVKVTVP DSNIDKMRVD YVNWKGPKYN NKLVKRFVSQ FLLFRKEEKE KNEKEALLKA SELVSGMGDK LGEYLGVKYK NVAKEVANDI KNFHGRNIRS YNEAMASLNK VLANPKMKVN KSDKDAIVNA WKQVNAKDMA NKIGNLGKAF KVADLAIKVE KIREKSIEGY NTGNWGPLLL EVESWIIGGV VAGVAISLFG AVLSFLPISG LAVTALGVIG IMTISYLSSF IDANRVSNIN NIISSVIRSS HHHHHH

Experimental information

• Beam: Instrument name: ESRF BM29 / City: Grenoble / 国: France / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.15 Å / Dist. spec. to detc.: 2.85 mm
• Detector: Name: Pilatus 1M / Type: Dectris / Pixsize x: 172 mm

Scan

Title: Colicin N delta 1-39 / Measurement date: Jun 29, 2012 / Storage temperature: 4 °C / Cell temperature: 4 °C / Exposure time: 2 sec. / Number of frames: 10 / Unit: 1/nm /

	Min	Max
Q	0.0922	4.5446

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 987 /

	Min	Max
Q	0.14107	3.84477
P(R) point	1	987
R	0	8.95

Result

Type of curve: merged
Comments: The results obtained from the bayesapp estimation of distribution functions from small-angle scattering data (http://www.bayesapp.org/) are included in the full entry zip archive.

	Experimental	Standard	Standard error	Porod
MW	39.213 kDa	33.75 kDa	2.25	-
Volume	-	-	-	60.37 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	33.6	0.44	33.58	0.36
Radius of gyration, Rg	2.75 nm	0.039	2.71 nm	0.56

	Min	Max	Error
D	-	8.95	0.1
Guinier point	14	95	-