5UF3

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

Summary for 5UF3

• Entry DOI: 10.2210/pdb5uf3/pdb
• NMR Information: BMRB: 30224
• Descriptor: phage GA operator RNA hairpin (1 entity in total)
• Functional Keywords: phage, rna hairpin, tetraloop, (a-a)-u motif, rna
• Biological source: Enterobacteria phage GA
• Total number of polymer chains: 1
• Total formula weight: 7394.50

Authors

Chang, A.T.,Tran, M.,DeJong, E.,Nikonowicz, E.P. (deposition date: 2017-01-03, release date: 2017-05-31, Last modification date: 2024-05-01)

Primary citation

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

Experimental method

SOLUTION NMR