Home
Database
Research
About us
RF-1-aptamer
Description
In 2007, Sando et al. selected the class II-1 aptamer against gel-immobilized Escherichia coli release factor 1 (RF-1) responsible for translation termination at amber (UAG) stop codon using a pool of 84-nt RNAs containing a randomized sequence of 50 nt[1].SELEX
In 2007, Suenaga et al. identified isolated specific sequences for targeting HA in a 84nt sequence pool through 11 rounds of selection[1].
Detailed information are accessible on SELEX page.
Structure
Class II-1 was the aptamer sequence mainly studied in the article, which had a high affinity with RF 1. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC-3'
Ligand information
SELEX ligand
This entry represents peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. This entry also includes chloroplast release factor APG3, which is an orthologue of E. coli RF1 and is essential for chloroplast development. APG3 could complement E. coli RF1 mutants, but not RF2 mutants, indicating that AP3 may function as RF1 in E. coli, showing specificity of stop codon recognition.-----from Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| release factor 1 (RF-1) | Q9X183 | IPR004373 | 119.15 kDa | MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVLGIGASVEEK | 1RQ0 | WP_004081559.1 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| class II-1 aptamer | 5'-GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC-3' | RF 1 | 30 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 |
|---|---|---|---|
| 1GQE-A | 25.7 | 4.8 | Release factor 2 |
| 5U4J-V | 14.1 | 2.7 | 16S rrna |
| 4NEY-B | 5.6 | 4.4 | Engineered protein or277 |
| 2RSM-A | 5.5 | 5.5 | Probable peptide chain release factor c12orf65 HO |
| 4KYZ-A | 5.2 | 8.6 | Designed protein or327 |
| 3LAY-J | 4.9 | 5.0 | Zinc resistance-associated protein |
| 4UER-J | 4.8 | 3.4 | Eif1a |
| 6D3G-C | 4.6 | 13.4 | Beta-lactamase |
| 6ELU-A | 4.6 | 3.3 | Serum resistance associated VSG protein |
| 1U8S-B | 4.5 | 4.6 | Glycine cleavage system transcriptional |
References
[1] In vitro selection of RNA aptamer against Escherichia coli release factor 1.Suenaga, E., & Kumar, PK. Sando, S., Ogawa, A., Nishi, T., Hayami, M., & Aoyama, Y.
Bioorganic & Medicinal Chemistry Letters,17(5):1216-20. (2007)