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CsrA-aptamer
Description
In 2005, Ashok K. Dubey and colleagues used in vitro selection to isolate RNA aptamers that bind to CsrA. CsrA of Escherichia coli is an RNA binding protein that plays a central role in repressing several stationary phase processes and activating certain exponential phase functions. Both the primary sequence and secondary structure of selected RNA ligands are important for high-affinity CsrA interaction[1].SELEX
In 2005, Ashok K. Dubey et al. isolated high-affinity RNA ligands containing single CsrA binding sites by 12 cycles of iterative selection[1].
Detailed information are accessible on SELEX page.
Structure
The aptamers containing single high affinity CsrA binding sites. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GGGAAUUCAACUCCAUCUAGGCACAAGGAUGUGCCAUAGUACUACAAGCU-3'
Ligand information
SELEX ligand
The RNA-binding protein CsrA (carbon storage regulator) is a new kind of global regulator, which facilitates specific mRNA decay. CsrA is entirely contained within a globular complex of approximately 18 CsrA-H6 subunits and a single RNA, CsrB. CsrA binds to the CsrB RNA molecule to form the Csr regulatory system which has a strong negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect on glycolysis.-----from Pfam| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| CsrA | P69913 | IPR003751 | 6.86 kDa | MLILTRRVGETLMIGDEVTVTVLGVKGNQVRIGVNAPKEVSVHREEIYQRIQAEKSQQSSY | 1Y00 | LC033559.1 |
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| R9-43 | 5'-GGGAAUUCAACUCCAUCUAGGCACAAGGAUGUGCCAUAGUACUACAAGCU-3' | CsrA | 7 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 |
|---|---|---|---|
| 1Y00-A | 12.1 | 0.0 | Carbon storage regulator |
| 1Y00-B | 10.5 | 0.9 | Carbon storage regulator |
| 2MF1-A | 4.0 | 5.9 | Carbon storage regulator homolog |
| 2JPP-B | 3.9 | 4.1 | Structural basis of RsmA/CsrA RNA recognition |
| 2MF0-A | 3.9 | 4.7 | Carbon storage regulator homolog |
| 2MF0-F | 3.8 | 5.1 | Carbon storage regulator homolog |
| 2MF0-D | 3.8 | 4.6 | Carbon storage regulator homolog |
| 2MF1-B | 3.8 | 4.8 | Carbon storage regulator homolog |
| 2MF0-B | 3.8 | 4.8 | Carbon storage regulator homolog |
| 2MF0-E | 3.7 | 5.1 | Carbon storage regulator homolog |
References
[1] RNA sequence and secondary structure participate in high-affinity CsrA-RNA interaction.Dubey, A. K., Baker, C. S., Romeo, T., & Babitzke, P.
RNA (New York, N.Y.), 11(10), 1579–1587. (2005)