Glycoprotein 2 (GP2) protein-aptamer

•

横向排列的点击按钮

Description

 In 2014, Misaho Hanazato and colleagues used SELEX (Systematic Evolution of Ligands by Exponential enrichment) technique to isolate high affinity RNA aptamers that bind to the GP2 protein[1].

SELEX

In 2014, Misaho Hanazato, Gaku Nakato, et al. isolated 11 specific sequences targeting Glycoprotein 2 (GP2) protein after 10 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'-GGGAGAAUUCCGACCAGAAGCAAGUAGUUGGCGCCUACUAUAGAAAUACGCCUUUCCUCUCUCCUUCCUCUUCU-3'

 drawing


Ligand information

SELEX ligand

Functions as an intestinal M-cell transcytotic receptor specific of type-I-piliated bacteria that participates in the mucosal immune response toward these bacteria. At the apical membrane of M-cells it binds fimH, a protein of the bacteria type I pilus tip. Internalizes bound bacteria, like E.coli and S.typhimurium, from the lumen of the intestine and delivers them, through M-cells, to the underlying organized lymphoid follicles where they are captured by antigen-presenting dendritic cells to elicit a mucosal immune response.
Name Uniprot ID Pfam MW Amino acids sequences PDB Gene ID
Glycoprotein 2 Q9D733 PF00100 59.154 kDa MVGCDLLWLAAASCVLTLVSPSTIHQGYGRPRNSSNLDLDCGSPDSPSSGICFDPCQNHTVLNDPTRSTENNDSSVAWCDDNLHGWYRFVGDGGVKMPETCVSVFRCHTSAPMWLSGSHPILGDGIVSHTACANWNENCCFWRSEVQVKACSEELGEYHVYKLQGTPECSLRYCTDPSTAPKNCEITCRPEEECVFQNNNWSCVCRQDLHVSDSQSLQPLLDCGDNEIKVKLDKCLLGGMGFKEEIIAYLNDRNCNGTMQDEPNNWVSMTSPVVANYCGNILEKNGTHAIYRNTLSLATDFIIRDFRVNVNFQCAYPLDMSVSLETALQPIVSSLTVDVDGAGEFNVKMALFQDQSYTNPYEGAEVLLPVESILYVGVLLNRGDTSRFKLLLTNCYATPSEDRHDPVKYFIIKNRCPNQRDSTINVRENGVSSESRFSVQMFMFAGNYDLVFLHCEVYLCDSTTEQCQPSCSTNRLRSSRPAIDYNRVLDLGPITKRSAQSSATSKGTPHTTGFLLAWPMFFLPVFLALLF 7P6R 2813
Some isolated sequences bind to the affinity of the protein.
Name Sequence Ligand Affinity
Apt1 5'-GGGAGAAUUCCGACCAGAAGCAAGUAGUUGGCGCCUACUAUAGAAAUACGCCUUUCCUCUCUCCUUCCUCUUCU-3' Glycoprotein 2 110±2.6 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
7PFP-A 20.1 1.6 Uromodulin
7C79-B 2.7 3.8 Ribonuclease mrp rna subunit nme1
7BCZ-A 2.5 4.0 4'-phosphopantetheinyl transferase entd
3TTG-A 2.4 3.1 Putative aminomethyltransferase
7XP3-A 2.4 4.1 Nac domain-containing protein 92
3DF6-B 2.3 3.6 Orf99
4QVH-A 2.3 3.8 Maltose-binding periplasmic protein, 4'-phosphopa
5A1U-E 2.3 3.9 Adp-ribosylation factor 1
6LE0-A 2.3 2.7 Abmu
6OOC-B 2.2 3.3 Dirigent


References

[1] Selection of an aptamer against mouse GP2 by SELEX.
Hanazato, M., Nakato, G., Nishikawa, F., Hase, K., Nishikawa, S., & Ohno, H
Cell structure and function, 39(1), 23-29. (2014)