Protein tyrosine phosphatases aptamer

•

横向排列的点击按钮

Description

 In 1998, Sabine D. Bell and colleagues used in vitro selection to isolate RNA aptamers that bind to the Protein tyrosine phosphatases. The aptamers localize to the protein active site and inhibit enzymatic activity[1].

SELEX

In 1998, Sabine D. Bell et al. isolated RNA aptamers that could bind tightly and specifically to Yop51*D162 through eight rounds of screening from two pools that contained random regions of either 30 (N30) or 71 (N71) nucleotides in length[1].
Detailed information are accessible on SELEX page.



Structure

The anti-Yop51* aptamers bind at or near the protein active site. The 2D structure of the figure is based on the article by ribodraw tool to draw[1].

5'-GGGAGATACCAGCTTATTCAATTCTGGCAATGGGTTATCCCAAGTGCTAAGCTTCAGGGAGCGAGGACCAGACGACGTACCTAACCCTAAGGTGAGATAGTAAGTGCAATCT-3'

 drawing


Ligand information

SELEX ligand

Yersinia outer protein H (YopH) belongs to the family of classical tyrosine-specific protein tyrosine phosphatases (PTPs). PTPs (EC 3.1.3.48) catalyze the dephosphorylation of phosphotyrosine peptides. YopH is an essential virulence determinant of the pathogenic bacterium by dephosphorylating several focal adhesion proteins including p130Cas in human epithelial cells, resulting in the disruption of focal adhesions and cell detachment from the extracellular matrix. It contains an N-terminal domain that contains signals required for TTSS-mediated delivery of YopH into host cells and a C-terminal catalytic PTP domain.-----from Pfam

Name Uniprot ID Pfam MW Amino acids sequences PDB Gene ID
Protein tyrosine phosphatases(PTPases) P15273 CD14559 33.52 kDa MRERPHTSGHHGAGEARATAPSTVSPYGPEARAELSSRLTTLRNTLAPATNDPRYLQACGGEKLNRFRDIQCRRQTAVRADLNANYIQVGNTRTIACQYPLQSQLESHFRMLAENRTPVLAVLASSSEIANQRFGMPDYFRQSGTYGSITVESKMTQQVGLGDGIMADMYTLTIREAGQKTISVPVVHVGNWPDQTAVSSEVTKALASLVDQTAETKRNMYESKGSSAVADDSKLRPVIHCRAGVGRTAQLIGAMCMNDSRNSQLSVEDMVSQMRVQRNGIMVQKDEQLDVLIKLAEGQGRPLLNS 1YTN 66841085

Affinity of anti-Yop51* Aptamers for Yop51*Δ162 was determined by nitrocellulose filter-binding assays. Some isolated sequences bind to the affinity of the protein.

Name Sequence Ligand Affinity
N30yc5 5'-GGGAATGGATCCACATCTACGTATTACTGCTGGTGACGAGGGCTAGACGACGTACCTTCACTGCAGACTTGACGAAGCTT-3' PTPases 28 nM
N71yc16 5'-GGGAGATACCAGCTTATTCAATTCTGGCAATGGGCTATCCCAAGTGCTAGGCTTCAGGGAGCGAGGACCAGACGACGTACCTAACCCTAAGGTGAGATAGTAAGTGCAATCT-3' PTPases 18 nM
drawing


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
1XXP-A 48.0 0.4 Protein-tyrosine phosphatases yoph
1G4U-S 27.0 2.0 Protein tyrosine phosphatases sptp
6UZT-A 25.1 2.6 receptor-type tyrosine-protein phosphatases alpha
3PS5-A 24.6 2.8 Tyrosine-protein phosphatases non-receptor type 6


References

[1] RNA molecules that bind to and inhibit the active site of a tyrosine phosphatase.
Bell, S. D., Denu, J. M., Dixon, J. E., & Ellington, A. D.
The Journal of biological chemistry, 273(23), 14309–14314. (1998)