PDBsum entry 1a51

RNA

PDB id: 1a51

Contents

DNA/RNA

PDB id:

1a51

Name:

RNA

Title:

Loop d/loop e arm of e. Coli 5s rrna, nmr, 9 structures

Structure:

5s rrna loop d/loop e. Chain: a. Fragment: loop d/loop e arm. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Cellular_location: cytoplasm. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

9 models

Authors:

A.Dallas,P.B.Moore

Key ref:

A.Dallas and P.B.Moore (1997). 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, 5, 1639-1653. PubMed id: 9438864 DOI: 10.1016/S0969-2126(97)00311-0

Date:

19-Feb-98 Release date: 27-May-98

DNA/RNA chain

G-G-C-C-G-A-U-G-G-U-A-G-U-G-U-G-G-G-G-U-C-U-C-C-C-C-A-U-G-C-G-A-G-A-G-U-A-G-G- 41 bases

DOI no: 10.1016/S0969-2126(97)00311-0

Structure 5:1639-1653 (1997)

PubMed id: 9438864

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.

A.Dallas, P.B.Moore.

ABSTRACT

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.

Selected figure(s)

Figure 5.
Figure 5. Stereo diagrams of the average structure of AD3 RNA. (a) The average structure of AD3 with regions of noncanonical structure elements shaded according to the color-coding in Figure 1c: helices IV and V are colored gray, the palindromic ends of loop E are yellow, the central base pairs of loop E are dark blue, the tandem GU wobbles purple, and loop D is colored green. (b) A heavy-atom only, CPK, space-filling representation of the average structure of AD3. Atoms are colored by type (nitrogen in blue, oxygen in red, phosphorus in magenta and carbon in gray). Superposition of (c) the loop E residues (72-78, 98-104) and (d) loop D-helix IV residues (79-97) from the nine structures generated by TAMD on the average structure. The average pairwise root mean square deviation between each structure and the average for loop E residues and loop D-helix IV residues is 0.90 Å and 0.55 Å, respectively.

The above figure is reprinted by permission from Cell Press: Structure (1997, 5, 1639-1653) copyright 1997.

Figure was selected by an automated process.