1YG4

Solution Structure of the ScYLV P1-P2 Frameshifting Pseudoknot, Regularized Average Structure

1YG4 の概要

• エントリーDOI: 10.2210/pdb1yg4/pdb
• 関連するPDBエントリー: 1YG3
• NMR情報: BMRB: 6509
• 分子名称: ScYLV RNA pseudoknot (1 entity in total)
• 機能のキーワード: rna pseudoknot; ribosomal frameshifting; protonated cytidine, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 9000.48

構造登録者

Cornish, P.V.,Hennig, M.,Giedroc, D.P. (登録日: 2005-01-04, 公開日: 2005-12-13, 最終更新日: 2024-05-22)

主引用文献

Cornish, P.V.,Hennig, M.,Giedroc, D.P.
A loop 2 cytidine-stem 1 minor groove interaction as a positive determinant for pseudoknot-stimulated -1 ribosomal frameshifting
Proc.Natl.Acad.Sci.USA, 102:12694-12699, 2005

PubMed Abstract: The molecular determinants of stimulation of -1 programmed ribosomal frameshifting (-1 PRF) by RNA pseudoknots are poorly understood. Sugarcane yellow leaf virus (ScYLV) encodes a 28-nt mRNA pseudoknot that promotes -1 PRF between the P1 (protease) and P2 (polymerase) genes in plant luteoviruses. The solution structure of the ScYLV pseudoknot reveals a well ordered loop 2 (L2) that exhibits continuous stacking of A20 through C27 in the minor groove of the upper stem 1 (S1), with C25 flipped out of the triple-stranded stack. Five consecutive triple base pairs flank the helical junction where the 3' nucleotide of L2, C27, adopts a cytidine 27 N3-cytidine 14 2'-OH hydrogen bonding interaction with the C14-G7 base pair. This interaction is isosteric with the adenosine N1-2'-OH interaction in the related mRNA from beet western yellows virus (BWYV); however, the ScYLV and BWYV mRNA structures differ in their detailed L2-S1 hydrogen bonding and L2 stacking interactions. Functional analyses of ScYLV/BWYV chimeric pseudoknots reveal that the ScYLV RNA stimulates a higher level of -1 PRF (15 +/- 2%) relative to the BWYV pseudoknot (6 +/- 1%), a difference traced largely to the identity of the 3' nucleotide of L2 (C27 vs. A25 in BWYV). Strikingly, C27A ScYLV RNA is a poor frameshift stimulator (2.0%) and is destabilized by approximately 1.5 kcal x mol(-1) (pH 7.0, 37 degrees C) with respect to the wild-type pseudoknot. These studies establish that the precise network of weak interactions nearest the helical junction in structurally similar pseudoknots make an important contribution to setting the frameshift efficiency in mRNAs.

PubMed: 16123125
DOI: 10.1073/pnas.0506166102

実験手法

SOLUTION NMR