2JSE

NMR reveals absence of hydrogen bonding in adjacent UU and AG mismatches in an isolated internal loop from ribosomal RNA.

2JSE の概要

• エントリーDOI: 10.2210/pdb2jse/pdb
• 分子名称: RNA (5'-R(*GP*GP*AP*GP*UP*GP*GP*CP*CP*GP*AP*AP*AP*GP*GP*CP*AP*UP*CP*UP*CP*C)-3') (1 entity in total)
• 機能のキーワード: nmr structure of rna loop 5' gugg 3' / 3' cuac 5', g base flipped out, 2x2 thermodynamics, lack of hydrogen bonding, absence of hydrogen bonding, uu internal loop, uu/ag internal loop, ag internal loop, internal loop from protein l11 binding site, rna
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 7112.31

構造登録者

Shankar, N. (登録日: 2007-07-03, 公開日: 2007-11-20, 最終更新日: 2024-05-29)

主引用文献

Shankar, N.,Xia, T.,Kennedy, S.D.,Krugh, T.R.,Mathews, D.H.,Turner, D.H.
NMR Reveals the Absence of Hydrogen Bonding in Adjacent UU and AG Mismatches in an Isolated Internal Loop from Ribosomal RNA
Biochemistry, 46:12665-12678, 2007

PubMed Abstract: NMR studies provide insights into structural features of internal loops. These insights can be combined with thermodynamic studies to generate models for predicting structure and energetics. The tandem mismatch internal loop, 5'GUGG3'(3'CUAC5'), has been studied by NMR. The NMR structure reveals an internal loop with no hydrogen bonding between the loop bases and with the G in the AG mismatch flipped out of the helix. The sequence of this internal loop is highly conserved in rRNA. The loop is located in the large ribosomal subunit and is part of a conserved 58-nt fragment that is the binding domain of ribosomal protein L11. Structural comparisons between variants of this internal loop in crystal structures of the 58-nt domain complexed with L11 protein and of the large ribosomal subunit (LSU) suggest that this thermodynamically destabilizing internal loop is partially preorganized for tertiary interactions and for binding L11. A model for predicting the base pairing and free energy of 2 x 2 nucleotide internal loops with a purine-purine mismatch next to a pyrimidine-pyrimidine mismatch is proposed on the basis of the present NMR structure and previously reported thermodynamics.

PubMed: 17929882
DOI: 10.1021/bi700802s

実験手法

SOLUTION NMR