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Peptide release factor 1-aptamer
Description
In 2002, Karol Szkaradkiewicz and colleagues used in vitro selection to isolate RNA aptamers that bind to the Thermus thermophilus release factor 1 (RF1). T. thermophilus RF1 recognizes UAG stop codons in an Escherichia coli in vitro translation system. Aptamers inhibited this RF1 activity[1].SELEX
In 2002, Karol Szkaradkiewicz et al. isolated sequences that bind to T. thermophilus RF1 by eight rounds of selection[1].
Detailed information are accessible on SELEX page.
Structure
The minimal structures of RNA aptamers that confer binding to RF1 consist of a hairpin with the unpaired RF1-interacting sequence. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GUGUGUCAAGCCAGCCCUAGCUUGCUACCUGGGGGCCACUGACCUAU-3'
Ligand information
SELEX ligand
Peptide chain release factors (RFs) are required for the termination of protein biosynthesis. At present two classes of RFs can be distinguished. Class I RFs bind to ribosomes that have encountered a stop codon at their decoding site and induce release of the nascent polypeptide. Class II RFs are GTP-binding proteins that interact with class I RFs and enhance class I RF activity. In prokaryotes there are two class I RFs that act in a codon specific manner: RF-1(gene prfA) mediates UAA and UAG-dependent termination while RF-2 (gene prfB) mediates UAA and UGA-dependent termination. RF-1 and RF-2 are structurally and evolutionary related proteins which have been shown to be part of a larger family.-----From Pfam
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Peptide release factor 1 | Q9X183 | IPR000352 | 39.66 kDa | MKEKKKEIEKLLARPDLTPEQMKNYGMEYAKIEEIENITNRIKETQEFIELLREEGENELEIEKYEKELDQLYQELLFLLSPEASDKAIVEIRPGTGGEEAALFARDLFRMYTRYAERKGWNLEVAEIHETDLGGIREVVFFVKGKNAYGILKYESGVHRVQRVPVTESGGRIHTSTATVAVLPEIEEKDIEIRPEDLKIETFRASGHGGQYVNKTESAVRITHLPTGIVVSCQNERSQYQNKQTALRILRARLYQLQKEQKEREISQKRKSQIGTGERSEKIRTYNFPQNRVTDHRINYTSYRLQEILDGDLDEIISKLIEHDIENNLEEVLGIGASVEEK | 1RQ0 | 3169506 |
Analysis of complexes formed by aptamers and RF1 by electrophoretic shift assay.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| RNA-5 | 5'-GUGUGUCAAGCCAGCCCUAGCUUGCUACCUGGGGGCCACUGACCUAU-3' | Thermus thermophilus release factor 1 | 20 μM |
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 | Possible 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 | Eifia |
| 6D3G-C | 4.6 | 13.4 | Beta-lactamase |
| 6ELU-A | 4.6 | 3.3 | Serum resistance associated； vsg peotein |
| 8DFV-K | 4.5 | 6.0 | Endoribonuclease dcr-1 |
References
[1] RNA aptamers directed against release factor 1 from Thermus thermophilus.Szkaradkiewicz, K., Nanninga, M., Nesper-Brock, M., Gerrits, M., Erdmann, V. A., & Sprinzl, M.
FEBS letters, 514(1), 90–95. (2002)