Structure and Dynamics of the Tetra-A Loop and (A-A)-U Sequence Motif within the Coliphage GA Replicase RNA Operator
Chang, Andrew T.; Tran, Michelle; Nikonowicz, Edward P.
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.