1k5i
From Proteopedia
(New page: 200px<br /><applet load="1k5i" size="450" color="white" frame="true" align="right" spinBox="true" caption="1k5i" /> '''NMR Structure of a Ribosomal RNA Hairpin Con...) |
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| - | [[Image:1k5i.gif|left|200px]]<br /><applet load="1k5i" size=" | + | [[Image:1k5i.gif|left|200px]]<br /><applet load="1k5i" size="350" color="white" frame="true" align="right" spinBox="true" |
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'''NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop'''<br /> | '''NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The structure of a 23 nt RNA sequence, rGGACCCGGGCUCAACCUGGGUCC, was | + | The structure of a 23 nt RNA sequence, rGGACCCGGGCUCAACCUGGGUCC, was elucidated using homonuclear NMR, distance geometry and restrained molecular dynamics. This RNA is analogous to residues 612-628 of the Escherichia coli 16S rRNA. The structure of the RNA reveals the presence of a pentaloop closed by a duplex stem in typical A-form conformation. The loop does not form a U-turn motif, as previously predicted. A non-planar A.C.A triple base interaction (hydrogen bonds A13 NH6-C10 O2 and C10 N3-A14 NH6) stabilizing the loop structure is inferred from structure calculations. The CUCAA loop structure is asymmetrical, characterized by a reversal of the phosphodiester backbone at the UC step (hydrogen bond C12 NH4-C10 O2') and 3'-stacking within the CAA segment. Loop base U11 is oriented towards the major groove and the consecutive adenosines on the 3'-end of the loop are well stacked, exposing their reactive functional groups in the minor groove defined by the duplex stem. The solution structure of the loop resembles that seen in the 3.3 A X-ray structure of the entire 30S subunit, where the analogous loop interacts with a ribosomal protein and a receptor RNA helix. |
==About this Structure== | ==About this Structure== | ||
| - | 1K5I is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http:// | + | 1K5I is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1K5I OCA]. |
==Reference== | ==Reference== | ||
NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop., Nagaswamy U, Gao X, Martinis SA, Fox GE, Nucleic Acids Res. 2001 Dec 15;29(24):5129-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11812846 11812846] | NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop., Nagaswamy U, Gao X, Martinis SA, Fox GE, Nucleic Acids Res. 2001 Dec 15;29(24):5129-39. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11812846 11812846] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Fox, G | + | [[Category: Fox, G E.]] |
[[Category: Gao, X.]] | [[Category: Gao, X.]] | ||
| - | [[Category: Martinis, S | + | [[Category: Martinis, S A.]] |
[[Category: Nagaswamy, U.]] | [[Category: Nagaswamy, U.]] | ||
[[Category: cucaa pentaloop]] | [[Category: cucaa pentaloop]] | ||
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[[Category: rna hairpin]] | [[Category: rna hairpin]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:30:22 2008'' |
Revision as of 11:30, 21 February 2008
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NMR Structure of a Ribosomal RNA Hairpin Containing a Conserved CUCAA Pentaloop
Overview
The structure of a 23 nt RNA sequence, rGGACCCGGGCUCAACCUGGGUCC, was elucidated using homonuclear NMR, distance geometry and restrained molecular dynamics. This RNA is analogous to residues 612-628 of the Escherichia coli 16S rRNA. The structure of the RNA reveals the presence of a pentaloop closed by a duplex stem in typical A-form conformation. The loop does not form a U-turn motif, as previously predicted. A non-planar A.C.A triple base interaction (hydrogen bonds A13 NH6-C10 O2 and C10 N3-A14 NH6) stabilizing the loop structure is inferred from structure calculations. The CUCAA loop structure is asymmetrical, characterized by a reversal of the phosphodiester backbone at the UC step (hydrogen bond C12 NH4-C10 O2') and 3'-stacking within the CAA segment. Loop base U11 is oriented towards the major groove and the consecutive adenosines on the 3'-end of the loop are well stacked, exposing their reactive functional groups in the minor groove defined by the duplex stem. The solution structure of the loop resembles that seen in the 3.3 A X-ray structure of the entire 30S subunit, where the analogous loop interacts with a ribosomal protein and a receptor RNA helix.
About this Structure
1K5I is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
NMR structure of a ribosomal RNA hairpin containing a conserved CUCAA pentaloop., Nagaswamy U, Gao X, Martinis SA, Fox GE, Nucleic Acids Res. 2001 Dec 15;29(24):5129-39. PMID:11812846
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