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polβ-aptamer
Description
In 2006, Gening, L. V., & Miller, H. obtained RNA aptamers for polbeta from a variable pool of 8 x 10(12) individual RNA sequences containing 30 random nucleotides, using in vitro selection.A total of 60 individual clones selected after seven rounds were screened for the ability to inhibit polbeta activity. All of the inhibitory aptamers analyzed have a predicted tri-lobed structure[1].SELEX
In 2006, Gening, L. V., & Miller, H. obtained RNA aptamers for polβ from a variable pool of 8 × 1012 individual RNA sequences containing 30 random nucleotides, Using in vitro selection. A total of 60 individual clones selected after seven rounds were screened for the ability to inhibit polβ activity[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'-GGGAAUGGAUCCACAUCUACGAAUUCGGUUGGGUUGUCGUAGAUAGAGCGCUUCAAUUCACUGCAGACUUGACGAAGCUU-3'
Ligand information
SELEX ligand
Repair polymerase that plays a key role in base-excision repair .During this process, the damaged base is excised by specific DNA glycosylases, the DNA backbone is nicked at the abasic site by an apurinic/apyrimidic (AP) endonuclease, and POLB removes 5'-deoxyribose-phosphate from the preincised AP site acting as a 5'-deoxyribose-phosphate lyase (5'-dRP lyase); Through its DNA polymerase activity, it adds one nucleotide to the 3' end of the arising single-nucleotide gap.-----from InterPro
| Name | Uniprot ID | Pfam | MW | Amino acids sequences | PDB | Gene ID |
|---|---|---|---|---|---|---|
| polβ | P06746 | PF00680 | 38.18 kDa | MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE | 8C2P | 5423 |
Some isolated sequences bind to the affinity of the protein.
| Name | Sequence | Ligand | Affinity |
|---|---|---|---|
| aptamer32 | 5'-GGGAAUGGAUCCACAUCUACGAAUUCGGUUGGGUUGUCGUAGAUAGAGCGCUUCAAUUCACUGCAGACUUGACGAAGCUU-3' | polβ | 290 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 |
|---|---|---|---|
| 4I27-A | 27.4 | 3.8 | Dna nucleotidylexotransferase |
| 4P4O-A | 25.7 | 3.1 | Dna polymerase beta |
| 3AU2-A | 17.8 | 2.9 | Dna polymerase beta family (x family) |
| 3NYB-A | 17.5 | 2.8 | Dna polymerase beta-like protein |
| 5WU1-A | 9.0 | 4.0 | Poly(a) rna polymerase protein 2 |
| 6IW6-A | 8.8 | 4.2 | Speckle targeted pip5k1a-regulated poly(a) polyme |
| 6IW6-A | 8.6 | 8.9 | Terminal uridylyltransferase 4,terminal uridylylt |
| 3HJ1-B | 8.6 | 5.1 | Minor editosome-associated tutase |
| 3C66-A | 8.6 | 4.1 | Poly(a) polymerase |
| 4ZRL-A | 8.3 | 3.5 | Poly(a) rna polymerase gld-2 |
References
[1] RNA aptamers selected against DNA polymerase beta inhibit the polymerase activities of DNA polymerases beta and kappa.Gening, L. V., & Miller, H.
Nucleic acids research, 34(9), 2579–2586. (2006)