Two crystal forms of helix II of Xenopus laevis 5S rRNA with a cytosine bulge

The crystal structure of r(GCCACCCUG).r(CAGGGUCGGC), helix II of the Xenopu s laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 Angstrom (Form I, space group P4(2)2(1)2, a = b - 57.15 A ngstrom and c = 43.54 Angstrom) and 1.7 Angstrom (Form II, space group P4(3 )2(1)2, a = b = 32.78 Angstrom and c = 102.5 Angstrom), The helical regions of the nonamers are found in the standard A-RNA conformations and the two forms have an RMS deviation of 0.75 Angstrom. However, the cytosine bulge a dopts two significantly different conformations with an RMS deviation of 3. 9 Angstrom. In Form I, the cytosine bulge forms an intermolecular (C) under bar(+)*G.C triple in the major groove of a symmetry-related duplex with in termolecular hydrogen bonds between N4 (C) under bar and O6G, and between p rotonated N3(+)(C) under bar and N7G. In contrast, a minor groove (C) under bar*G.C triple is formed in Form II with intermolecular hydrogen bonds bet ween O2 (C) under bar and N2G, and between N3 (C) under bar and N3G with a water bridge. A partial major groove opening was observed in Form I structu re at the bulge site. Two Ca2+ ions were found in Form I helix whereas ther e were none in Form II. The structural comparison of these two forms indica tes that bulged residues can adopt a variety of conformations with little p erturbation to the global helix structure. This suggests that bulged residu es could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules.