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APC-99 aptamer
Description
Sang Wan Gal and Sergey Amontov et al. reported aptamers with affinity for APC-167 in their article published in 1998[1].SELEX
In their work published in 1998, Sang Wan Gal and Sergey Amontov et al. used SELEX to isolate RNA aptamer sequences with affinity for APC-167 from a nucleic acid library containing about 1013 sequences after 8 rounds of selection process[1].
Detailed information are accessible on SELEX page.
Structure
The 2D structure of the figure is based on the article by ribodraw tool to draw[1].5'-GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU-3'
Ligand information
SELEX ligand
Protein C is a vitamin K-dependent serine protease that regulates blood coagulation by inactivating factors Va and VIIIa in the presence of calcium ions and phospholipids. Exerts a protective effect on the endothelial cell barrier function.-----From Uniprot
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| APC | P04070 | PF00089 | 52.071 kDa | MWQLTSLLLFVATWGISGTPAPLDSVFSSSERAHQVLRIRKRANSFLEELRHSSLERECIEEICDFEEAKEIFQNVDDTLAFWSKHVDGDQCLVLPLEHPCASLCCGHGTCIDGIGSFSCDCRSGWEGRFCQREVSFLNCSLDNGGCTHYCLEEVGWRRCSCAPGYKLGDDLLQCHPAVKFPCGRPWKRMEKKRSHLKRDTEDQEDQVDPRLIDGKMTRRGDSPWQVVLLDSKKKLACGAVLIHPSWVLTAAHCMDESKKLLVRLGEYDLRRWEKWELDLDIKEVFVHPNYSKSTTDNDIALLHLAQPATLSQTIVPICLPDSGLAERELNQAGQETLVTGWGYHSSREKEAKRNRTFVLNFIKIPVVPHNECSEVMSNMVSENMLCAGILGDRQDACEGDSGGPMVASFHGTWFLVGLVSWGEGCGLLHNYGVYTKVSRYLDWIHGHIRDKEAPQKSWAP | 1AUT | 5624 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| APC-99 | 5'-GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU-3' | Human activated protein C | 120 nM |
| APC-167 | 5'-GGGAGAAUUCCGACCAGAAGCUUGUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCUUUGGGUUUUGUGAUUUGGUCAUAUGUGCGUCUACAUGGAUCCUCA-3' | Human activated protein C | 110 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 |
|---|---|---|---|
| 5TO3-B | 35.8 | 1.4 | Prothrombin |
| 1Z8G-A | 33.1 | 1.5 | Serine protease hepsin |
| 7WQX-A | 32.7 | 1.7 | Enteropeptidase |
| 3H7T-A | 29.1 | 2.1 | Group 3 allergen smipp-S Yvt004a06 |
| 4A5T-S | 28.6 | 2.2 | Plasminogen |
| 4KKD-B | 28.5 | 2.2 | Mannan-binding lectin serine protease 1 |
| 5I25-A | 27.4 | 2.1 | Coagulation factor XI |
| 3H5C-B | 26.3 | 2.3 | Protein Z-dependent protease inhibitor |
| 2XXL-B | 24.9 | 2.2 | Gram-positive specific serine protease, isoform B |
| 2XRC-B | 24.0 | 1.8 | Human complement factor I |
References
[1] Selection of a RNA aptamer that binds to human activated protein C and inhibits its protease function.Gal, S. W., Amontov, S., Urvil, P. T., Vishnuvardhan, D., Nishikawa, F., Kumar, P. K., & Nishikawa, S.
European journal of biochemistry, 252(3), 553–562. (1998)