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Restriction endonucleases (REases) KpnI-aptamer
Description
In 2015, Estefanía Mondragón and colleagues used SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique to isolate high affinity RNA aptamers that bind to the Reases KpnI protein[1].SELEX
In 2015, Estefanía Mondragón and L. James Maher, III isolated 10 specific sequences for targeting Restriction endonucleases (REases) in 20 rounds of selection[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'-GGGAUAUCCUUCAUGAUUCGGAAAAGCGUAACCGCGGCCAAUCAUGCAUGAAGCGUUCCAUAUUUUU-3'
Ligand information
SELEX ligand
The restriction endonucleases (REases) KpnI is an orthodox Type IIP enzyme, which binds to DNA in the absence of metal ions and cleaves the DNA sequence 5′-GGTAC^C-3′ in the presence of Mg2+ as shown generating 3′ four base overhangs.
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| Restriction endonucleases (REases) KpnI | P04062 | PF02055 | 59.716 kDa | MEFSSPSREECPKPLSRVSIMAGSLTGLLLLQAVSWASGARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ | 1OGS | 2629 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| anti-KpnI RNA Aptamer 20 | 5'-GGGAUAUCCUUCAUGAUUCGGAAAAGCGUAACCGCGGCCAAUCAUGCAUGAAGCGUUCCAUAUUUUU-3' | REases KpnI | 11.6 ± 2.3 nM |
| anti-KpnI RNA Aptamer 24 | 5'-GGGAUAUCCUUCAUGGUGUGAUUAAACGUAAUCUCAAUCGAUCAUGCAUGAAGCGUUCCAUAUUUUU-3' | REases KpnI | 28.7 ± 5.2 nM |
| anti-KpnI RNA Aptamer 29 | 5'-GGGAUAUCCCUACAUGAUAAUCGGGUGAGUAAGGCCUAAACAUCAUGCAUGAAGCGUUCCAUAUUUUU-3' | REases KpnI | 419 ± 46.6 nM |
| anti-KpnI RNA Aptamer 30 | 5'-GGGAUAUCCUUCAUGAUUCGGAAAAGCGUAACCGCGGCCGAUCAUGCAUGAAGCGUUCCAUAUUUUU-3' | REases KpnI | 18.6 ± 4.5 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 |
|---|---|---|---|
| 2V3E-A | 66.2 | 0.7 | Glucosylceramidase |
| 6KRN-A | 37.0 | 2.1 | Mating factor alpha,gh30 xylanase b |
| 4QAW-A | 33.0 | 2.1 | Xyn30d |
| 3CLW-A | 31.4 | 2.6 | Conserved exported protein |
| 5N8K-A | 27.9 | 2.4 | Galactocerebrosidase |
| 5JVK-A | 23.4 | 3.6 | Uncharacterized protein |
| 1R8L-B | 22.0 | 3.2 | Endo-beta-1,4-galactanase |
| 5BX9-A | 21.9 | 3.8 | Pslg |
| 2VRK-A | 21.7 | 2.8 | Alpha-l-arabinofuranosidase |
| 8I0A-A | 21.0 | 2.9 | Alpha-l-arabinofuranosidase |
References
[1] RNA aptamer inhibitors of a restriction endonuclease.Mondragón, E., & Maher III, L. J.
Nucleic acids research, 43(15), 7544-7555. (2015)