1a4d | pdb_00001a4d

LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRNA, NMR, MINIMIZED AVERAGE STRUCTURE

spinqualitylabelsall models 1a4d, 1 NMR models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 1a4d is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Related: 1a51 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed BACKGROUND: 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. RESULTS: 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 pyrimidine is fully exposed to solvent. CONCLUSIONS: This structure rationalizes all the biochemical and chemical protection data available 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 loop is highly irregular, and its irregularities may explain why the loop E-loop D arm of 5S rRNA interacts specifically with ribosomal protein L25 in E. coli. 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.,Dallas A, Moore PB Structure. 1997 Dec 15;5(12):1639-53. PMID:9438864 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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