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Pepocin aptamer
Description
In 2000, Hirao, I. et al. had isolated aptamers that target pepocin from a degenerate RNA pool through in vitro selection. These aptamers selectively bind to pepocin with dissociation constants ranging from 20 to 30 nM. Furthermore, they are capable of inhibiting the N-glycosidase activity of pepocin on rat liver 28 S rRNA[2].SELEX
Selection experiments were initiated with an RNA pool containing 2 × 1013 different sequences. The RNA pool that contained a region of 30 randomized nucleotides flanked by constant regions. After eight rounds of selection, the fraction of the pool which bound pepocin had increased from 0.03 to 24%. Twenty-six clones were isolated from the eighth round of selection. Twenty-three of these aptamers had a similar sequence and bound specifically to pepocin[2].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figures is based on the article by ribodraw tool to draw.5'-CAAGUCUAAUGUCGGACUCGAUAUCAAUUCACUGCAGACUUG-3'
Ligand information
SELEX ligand
Pepocin is a ribosome-inactivating protein (RIP). A ribosome-inactivating protein (RIP) is a protein synthesis inhibitor that acts at the eukaryotic ribosome. This protein family describes a large family of such proteins that work by acting as rRNA N-glycosylase (EC 3.2.2.22). They inactivate 60S ribosomal subunits by an N-glycosidic cleavage, which releases a specific adenine base from the sugar-phosphate backbone of 28S rRNA. RIPs exist in bacteria and plants.-----From WiKi
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Pepocin | P80750 | PF00161 | 27.0 KDa | NVRFDLSSATSSSYKTFIKNLREALPKDGKVYDIPVLLSTVMDSRRFILIDLVNYDGQSITAAIDVLNVYIVAYSTGTVSYFFQQVPAQAPKLLFKGTQQRTLPYTGNYENLQTAAKKLRENIELGLPALDSAITTLFHYNAEAAASALLVLIQTTSEAARFRYIELQIANNVGTKFKPSQTIISLENNWSALSKQIQIAKNKNGQFETPVILIDPQGNRVQITNVTSNVVTQNIQLLLNIGAT | 3BWH | 3663 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| 8-09 aptamer | 5'-CAAGUCUAAUGUCGGACUCGAUAUCAAUUCACUGCAGACUUG-3' | pepocin | 21 ± 2 nM |
| 8-14 aptamer | 5'-AGUCUAGGAAGCAGUCGGACUUGUUAUCAAUUCACUGCAGACU-3' | pepocin | 23.4 ± 2.3 nM |
| 9-41U22 | 5'-GGGAGUCUGAAGUCGGACUCGUUAUCAAUUCACUUCAGACU-3' | pepocin | 17.9 ± 2.2 nM |
Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and chose the top 10 in terms of similarity for presentation. The Dali server is a network service for comparing protein structures in 3D. Dali compares them against those in the Protein Data Bank (PDB). Z-score is a standard score that is converted from an original score. The list of neighbours is sorted by Z-score. Similarities with a Z-score lower than 2 are spurious. RMSD(Root Mean Square Deviation) value is used to measure the degree to which atoms deviate from the alignment position.
| PDB | Z-socre | RMSD | Description |
|---|---|---|---|
| 3BWH-A | 45.6 | 0.0 | Cucurmosin |
| 1MRJ-A | 40.8 | 0.7 | Alpha-trichosanthin |
| 1MRK-A | 40.8 | 0.7 | Alpha-trichosanthin |
| 1QD2-A | 40.6 | 0.7 | Trichosanthin |
| 1TCS-A | 40.5 | 0.7 | Trichosanthin |
| 1BRY-Y | 40.5 | 0.8 | Bryodin i |
| 6Z1Y-C | 40.4 | 0.7 | Trichobakin |
| 1BRY-Z | 40.4 | 0.8 | Bryodin i |
| 6Z1Y-D | 40.3 | 0.7 | Trichobakin |
| 1GIS-A | 40.2 | 0.8 | Ribosome-inactivating protein alpha |
References
[1] In vitro selection of aptamers that bind to ribosome-inactivating toxins.Hirao, I., Yoshinari, S., Yokoyama, S., Endo, Y., & Ellington, A. D.
Nucleic acids symposium series, (37), 283–284. (1997)
[2] RNA aptamers that bind to and inhibit the ribosome-inactivating protein, pepocin.
Hirao, I., Madin, K., Endo, Y., Yokoyama, S., & Ellington, A. D.
The Journal of biological chemistry, 275(7), 4943–4948. (2000)