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Ribosomal protein S8-aptamer
Timeline
An RNA aptamer identified by in vitro screening for TetR binding and in vivo screening for TetR inducible binding induces ter controlled gene expression in E. coli[1]
RNA aptamers adopt completely different secondary structures in the free and protein-bound states[2]
Description
In 1997, Moine Herve et al. performed in vitro iterative selection of RNA aptamers that bind S8. In 2014, Milya Davlieva et al. examined the structural accommodation of an RNA aptamer that binds bacterial r-protein S8[1,2].SELEX
In 2014, Milya Davlieva et al. isolated 40 sequences that do not maintain the conserved features of helix 21 but retain the ability to bind the S8 protein with high affinity and specificity through 10 rounds of selection[2].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we use ribodraw to complete the figure, through the 3D structure information[5].
5'-GGGAUGCUCAGUGAUCCUUCGGGAUAUCAGGGCAUCCC-3'
3D visualisation
Milya Davlieva et al. sovled the crystal structure, at 2.69 A resolution, of an RNA aptamer bound to Bacillus ribosomal S8 protein has been determined. The PDB ID of this structure is 4PDB[2].Additional available structures that have been solved and detailed information are accessible on Structures page.
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 4PDB at 2.69 Å resolution. ribosomal S8 protein (shown in vacuumm electrostatics), blue is positive charge, red is negative charge. Right: The hydrogen bonds of binding sites of the aptamer bound with ribosomal S8 protein.
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Ligand information
SELEX ligand
Milya Davlieva et al. investigated the affinity of the RNA aptamer via EMSA and ITC experiments[2].| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| RNA-2 aptamer | 5'-GGGAUGCUCAGUGAUCCUUCGGGAUAUCAGGGCAUCCC-3' | Bacillus ribosomal protein S8 | 110 ± 30 nM |
Structure ligand
This entry includes small ribosomal subunit protein uS8 from bacteria, archaea and eukaryotes (in yeast, these proteins are also known as S22 and in vertebrates S15A). In Escherichia coli, uS8 is known to bind directly to 16S ribosomal RNA. Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome.-----from Pfam
| Uniprot ID | Pfam | MW | Amino acids sequences | PDB ID | GenBank |
|---|---|---|---|---|---|
| P56209 | IPR035987 | 29.24 kDa | VMTDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLKYGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVIVMTDPIADMLTAIRNANMVRHEKLEVPASKIKREIAEILKREGFIRDYEYIEDNKQGILRIFLKYGPNERVITGLKRISKPGLRVYVKAHEVPRVLNGLGIAILSTSQGVLTDKEARQKGTGGEIIAYVI | 1SEI | 947802 |
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Similar compound
We used the Dail server website to compare the structural similarities of ligand proteins, and selected the previous information with high 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).
| PDB | Z-score | RMSD | Description |
|---|---|---|---|
| 3RF2-A | 18.5 | 1.9 | 30s ribosomal protein s8 |
| 8D8J-H | 18.2 | 1.8 | probable s-adenosyl-l-methioni |
| 7QIX-T | 17.2 | 2.2 | 18s rrna body |
| 1I6U-A | 17.1 | 2.2 | 16s rrna fragment |
| 6ZUO-W | 16.6 | 2.4 | pre-18s ribosomal rna |
| 7PWF-W | 16.4 | 2.3 | ribosomal protein s29a |
| 6WDR-W | 15.8 | 2.4 | 40s ribosomal protein a0-a |
| 7PKU-h | 13 | 2.9 | ms35 |
| 4OCH-A | 6.8 | 2.4 | endonuclease muts2 |
| 2A1S-C | 6.3 | 2.8 | poly(A)-specific ribonnuclease |
References
[1] The RNA binding site of S8 ribosomal protein of Escherichia coli: Selex and hydroxyl radical probing studies.Moine, H., Cachia, C., Westhof, E., Ehresmann, B., & Ehresmann, C.
RNA (New York, N.Y.), 3(3), 255–268. (1997)
[2] Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis.
Davlieva, M., Donarski, J., Wang, J., Shamoo, Y., & Nikonowicz, E. P.
Nucleic acids research, 42(16), 10795–10808. (2014)
[3] The intrinsic flexibility of the aptamer targeting the ribosomal protein S8 is a key factor for the molecular recognition.
Autiero, I., Ruvo, M., Improta, R., & Vitagliano, L.
Biochimica et Biophysica Acta (BBA)-General Subjects, 1862(4), 1006-1016. (2018)
[4] Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking.
Oliveira, R., Pinho, E., Sousa, A. L., Dias, Ó., Azevedo, N. F., & Almeida, C.
PloS one, 17(3), e0264701. (2022)
[5] Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.
Pavan, M., Bassani, D., Sturlese, M., & Moro, S.
NAR genomics and bioinformatics, 4(4), lqac088. (2022)