THE LOOP-E LOOP-D REGION OF ESCHERICHIA-COLI 5S RIBOSOMAL-RNA - THE SOLUTION STRUCTURE REVEALS AN UNUSUAL LOOP THAT MAY BE IMPORTANT FOR BINDING RIBOSOMAL-PROTEINS

Background: 5S ribosomal RNA is the smallest rRNA, Its Watson-Crick he lices 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 kingdom s, and is terminated by a pyrimidine-rich loop called loop D. Loop E i s the binding site for the ribosomal protein L25 in the E, coli riboso me. Results: The solution structure of a 42-nucleotide derivative of E . coli 5S rRNA that includes loops D and E has been determined by nucl ear magnetic resonance spectroscopy, Formally, loop E is not a loop at all; it is a double helical structure that contains seven, consecutiv e non-Watson-Crick base pairs. The major groove of the molecule is nar rowed in loop E, and an unusual array of hydrogen-bond donors and acce pters 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 ea ch other, and tilt into the minor groove of the adjacent helix. The th ird pyrimidine is fully exposed to solvent. Conclusions: This structur e rationalizes all the biochemical and chemical protection data availa ble for the loop E-loop D arm of intact 5S rRNA, While the molecule is double helical over its entire length, the geometry of its internal l oop is highly irregular, and its irregularities may explain why the lo op E-loop D arm of 5S rRNA interacts specifically with ribosomal prote in L25 in E. coli.