1a4d: Difference between revisions
New page: left|200px<br /><applet load="1a4d" size="450" color="white" frame="true" align="right" spinBox="true" caption="1a4d" /> '''LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRN... |
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'''LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRNA, NMR, MINIMIZED AVERAGE STRUCTURE'''<br /> | '''LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRNA, NMR, MINIMIZED AVERAGE STRUCTURE'''<br /> | ||
==Overview== | ==Overview== | ||
BACKGROUND: 5S ribosomal RNA is the smallest rRNA. Its Watson-Crick | 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. | ||
==About this Structure== | ==About this Structure== | ||
1A4D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http:// | 1A4D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1A4D OCA]. | ||
==Reference== | ==Reference== | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Dallas, A.]] | [[Category: Dallas, A.]] | ||
[[Category: Moore, P | [[Category: Moore, P B.]] | ||
[[Category: 5s rrna]] | [[Category: 5s rrna]] | ||
[[Category: cross-strand stack]] | [[Category: cross-strand stack]] | ||
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[[Category: translation]] | [[Category: translation]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:40:42 2008'' | ||
Revision as of 12:40, 21 February 2008
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LOOP D/LOOP E ARM OF ESCHERICHIA COLI 5S RRNA, NMR, MINIMIZED AVERAGE STRUCTURE
OverviewOverview
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.
About this StructureAbout this Structure
1A4D is a Protein complex structure of sequences from Escherichia coli. Full crystallographic information is available from OCA.
ReferenceReference
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
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