5UF3

Structure Effects of the Four-Adenine Loop of the Coliphage GA Replicase RNA Operator

5UF3 の概要

• エントリーDOI: 10.2210/pdb5uf3/pdb
• NMR情報: BMRB: 30224
• 分子名称: phage GA operator RNA hairpin (1 entity in total)
• 機能のキーワード: phage, rna hairpin, tetraloop, (a-a)-u motif, rna
• 由来する生物種: Enterobacteria phage GA
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 7394.50

構造登録者

Chang, A.T.,Tran, M.,DeJong, E.,Nikonowicz, E.P. (登録日: 2017-01-03, 公開日: 2017-05-31, 最終更新日: 2024-05-01)

主引用文献

Chang, A.T.,Tran, M.,Nikonowicz, E.P.
Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator.
Biochemistry, 56:2690-2700, 2017

PubMed Abstract: The three-dimensional structure of a RNA hairpin containing the RNA operator binding site for bacteriophage GA coat protein is presented. The phage GA operator contains the asymmetric (A-A)-U sequence motif and is capped by a four-adenine (tetra-A) loop. The uridine of the (A-A)-U motif preferentially pairs with the 5'-proximal cross-strand adenine, and the 3'-proximal adenine stacks into the helix. The tetra-A loop is well-ordered with adenine residues 2-4 forming a 3' stack. This loop conformation stands in contrast to the structure of the 5'-AUUA loop of the related phage MS2 operator in which residues 1 and 2 form a 5' stack. The context dependence of the (A-A)-U sequence motif conformation was examined using structures of 76 unique occurrences from the Protein Data Bank. The motif almost always has one adenine bulged and the other adenine adopting an A-U base pair. In the case in which the (A-A)-U motif is flanked by only one Watson-Crick base pair, the adenine adjacent to the flanking base pair tends to bulge; 80% of motifs with a 3' flanking pair have a 3' bulged adenine, and 84% of motifs with a 5' flanking pair have a 5' bulged adenine. The frequencies of 3'- and 5'-proximal adenines bulging are 33 and 67%, respectively, when the (A-A)-U motif is flanked by base pairs on both sides. Although a 3' flanking cytidine correlates (88%) with bulging of the 5'-proximal adenine, no strict dependence on flanking nucleotide identity was identified for the 5' side.

PubMed: 28488852
DOI: 10.1021/acs.biochem.7b00123

実験手法

SOLUTION NMR