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

Published online by Cambridge University Press:  01 September 2000

YONG XIONG
Affiliation:
The Ohio State University, Biological Macromolecular Structure Center, Departments of Chemistry, Biochemistry and Biophysics Program, Columbus, Ohio 43210, USA
MUTTAIYA SUNDARALINGAM
Affiliation:
The Ohio State University, Biological Macromolecular Structure Center, Departments of Chemistry, Biochemistry and Biophysics Program, Columbus, Ohio 43210, USA
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Abstract

The crystal structure of r(GCCACCCUG)[bull ]r(CAGGGUCGGC), helix II of the Xenopus laevis 5S rRNA with a cytosine bulge (underlined), has been determined in two forms at 2.2 Å (Form I, space group P42212, a = b = 57.15 Å and c = 43.54 Å) and 1.7 Å (Form II, space group P43212, a = b = 32.78 Å and c = 102.5 Å). 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 Å. However, the cytosine bulge adopts two significantly different conformations with an RMS deviation of 3.9 Å. In Form I, the cytosine bulge forms an intermolecular C+∗G[bull ]C triple in the major groove of a symmetry-related duplex with intermolecular hydrogen bonds between N4C and O6G, and between protonated N3+C and N7G. In contrast, a minor groove C∗G[bull ]C triple is formed in Form II with intermolecular hydrogen bonds between O2C and N2G, and between N3C and N3G with a water bridge. A partial major groove opening was observed in Form I structure at the bulge site. Two Ca2+ ions were found in Form I helix whereas there were none in Form II. The structural comparison of these two forms indicates that bulged residues can adopt a variety of conformations with little perturbation to the global helix structure. This suggests that bulged residues could function as flexible latches in bridging double helical motifs and facilitate the folding of large RNA molecules.

Type
Research Article
Information
RNA , Volume 6 , Issue 9 , September 2000 , pp. 1316 - 1324
Copyright
2000 RNA Society

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