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PDBsum entry 1a51
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References listed in PDB file
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Key reference
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Title
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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.
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Authors
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A.Dallas,
P.B.Moore.
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Ref.
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Structure, 1997,
5,
1639-1653.
[DOI no: ]
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PubMed id
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Abstract
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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.
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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.
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1639-1653)
copyright 1997.
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Headers
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