The loop E-loop D region of Escherichia coli 5S rRNA: the solution structure reveals an unusual loop that may be important for binding ribosomal proteins

Structure
A Dallas, P B Moore

Abstract

5S ribosomal RNA is the smallest rRNA. Its Watson-Crick helices were identified more than 20 years ago, but the conformations of its loops have long defied analysis. One of the three arms of 5S rRNA, residues 69-106 in Escherichia coli, contains a 14-residue internal loop called loop E. The sequence of loop E is conserved within kingdoms, and is terminated by a pyrimidine-rich loop called loop D. Loop E is the binding site for the ribosomal protein L25 in the E. coli ribosome. The solution structure of a 42-nucleotide derivative of E. coli 5S rRNA that includes loops D and E has been determined by nuclear magnetic resonance spectroscopy. Formally, loop E is not a loop at all; it is a double helical structure that contains seven, consecutive non-Watson-Crick base pairs. The major groove of the molecule is narrowed in loop E, and an unusual array of hydrogen-bond donors and acceptors appear in its minor groove. Loop D, which on paper looks like a three-pyrimidine terminal loop closed by a GC, is better thought of as a five-base loop because its closing GC is not a normal Watson-Crick pair. The two pyrimidines on the 5'-side of the loop are stacked on each other, and tilt into the minor groove of the adjacent helix. The third pyri...Continue Reading

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Citations

Dec 16, 2003·Journal of Molecular Biology·Pascal AuffingerEric Westhof
Dec 11, 2002·Journal of Molecular Biology·Jung C LeeRobin R Gutell
Jan 16, 2003·Journal of Molecular Biology·Pramodh Vallurupalli, Peter B Moore
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Jun 29, 2000·Annual Review of Biochemistry·P B Moore
May 18, 2004·RNA·Helen J MerianosPeter B Moore
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