2JUK

guanidino neomycin B recognition of an HIV-1 RNA helix

2JUK の概要

• エントリーDOI: 10.2210/pdb2juk/pdb
• 分子名称: HIV-1 frameshift site RNA, (1S,2R,3S,4R,6S)-4,6-bis{[amino(iminio)methyl]amino}-2-{[3-O-(2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranosyl)-beta-D-arabinofuranosyl]oxy}-3-hydroxycyclohexyl 2,6-bis{[amino(iminio)methyl]amino}-2,6-dideoxy-beta-L-glucopyranoside (2 entities in total)
• 機能のキーワード: hiv-1, rna-ligand interactions, guanidinoglycosides, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 7944.23

構造登録者

Staple, D.W.,Venditti, V.,Niccolai, N.,Elson-Schwab, L.,Tor, Y.,Butcher, S.E. (登録日: 2007-08-30, 公開日: 2007-11-20, 最終更新日: 2024-05-29)

主引用文献

Staple, D.W.,Venditti, V.,Niccolai, N.,Elson-Schwab, L.,Tor, Y.,Butcher, S.E.
Guanidinoneomycin B Recognition of an HIV-1 RNA Helix.
Chembiochem, 9:93-102, 2008

PubMed Abstract: Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.

PubMed: 18058789
DOI: 10.1002/cbic.200700251

実験手法

SOLUTION NMR