1syz
From Proteopedia
(New page: 200px<br /><applet load="1syz" size="450" color="white" frame="true" align="right" spinBox="true" caption="1syz" /> '''Solution structure of the S. Cerevisiae U6 i...) |
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| - | [[Image:1syz.gif|left|200px]]<br /><applet load="1syz" size=" | + | [[Image:1syz.gif|left|200px]]<br /><applet load="1syz" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="1syz" /> | caption="1syz" /> | ||
'''Solution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7'''<br /> | '''Solution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The U6 RNA intramolecular stem-loop (ISL) structure is an essential | + | The U6 RNA intramolecular stem-loop (ISL) structure is an essential component of the spliceosome and binds a metal ion required for pre-messenger RNA splicing. The metal binding internal loop region of the stem contains a partially protonated C67-(+)A79 base pair (pK(a) = 6.5) and an unpaired U80 nucleotide that is stacked within the helix at pH 7.0. Here, we determine that protonation occurs with an exchange lifetime of approximately 20 micros and report the solution structures of the U6 ISL at pH 5.7. The differences between pH 5.7 and 7.0 structures reveal that the pH change significantly alters the RNA conformation. At lower pH, U80 is flipped out into the major groove. Base flipping involves a purine stacking interaction of flanking nucleotides, inversion of the sugar pucker 5' to the flipped base, and phosphodiester backbone rearrangement. Analysis of residual dipolar couplings as a function of pH indicates that base flipping is not restricted to a local conformational change. Rather, base flipping alters the alignment of the upper and lower helices. The alternative conformations of the U6 ISL reveal striking structural similarities with both the NMR and crystal structures of domain 5 of self-splicing group II introns. These structures suggest that base flipping at an essential metal binding site is a conserved feature of the splicing machinery for both the spliceosome and group II self-splicing introns. |
==About this Structure== | ==About this Structure== | ||
| - | 1SYZ 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:// | + | 1SYZ 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=1SYZ OCA]. |
==Reference== | ==Reference== | ||
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[[Category: Abildgaard, F.]] | [[Category: Abildgaard, F.]] | ||
[[Category: Blad, H.]] | [[Category: Blad, H.]] | ||
| - | [[Category: Butcher, S | + | [[Category: Butcher, S E.]] |
| - | [[Category: Reiter, N | + | [[Category: Reiter, N J.]] |
[[Category: a-c wobble pair]] | [[Category: a-c wobble pair]] | ||
[[Category: gnra-like tetratloop]] | [[Category: gnra-like tetratloop]] | ||
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[[Category: stem-loop]] | [[Category: stem-loop]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:07:36 2008'' |
Revision as of 13:07, 21 February 2008
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Solution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7
Overview
The U6 RNA intramolecular stem-loop (ISL) structure is an essential component of the spliceosome and binds a metal ion required for pre-messenger RNA splicing. The metal binding internal loop region of the stem contains a partially protonated C67-(+)A79 base pair (pK(a) = 6.5) and an unpaired U80 nucleotide that is stacked within the helix at pH 7.0. Here, we determine that protonation occurs with an exchange lifetime of approximately 20 micros and report the solution structures of the U6 ISL at pH 5.7. The differences between pH 5.7 and 7.0 structures reveal that the pH change significantly alters the RNA conformation. At lower pH, U80 is flipped out into the major groove. Base flipping involves a purine stacking interaction of flanking nucleotides, inversion of the sugar pucker 5' to the flipped base, and phosphodiester backbone rearrangement. Analysis of residual dipolar couplings as a function of pH indicates that base flipping is not restricted to a local conformational change. Rather, base flipping alters the alignment of the upper and lower helices. The alternative conformations of the U6 ISL reveal striking structural similarities with both the NMR and crystal structures of domain 5 of self-splicing group II introns. These structures suggest that base flipping at an essential metal binding site is a conserved feature of the splicing machinery for both the spliceosome and group II self-splicing introns.
About this Structure
1SYZ is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Dynamics in the U6 RNA intramolecular stem-loop: a base flipping conformational change., Reiter NJ, Blad H, Abildgaard F, Butcher SE, Biochemistry. 2004 Nov 2;43(43):13739-47. PMID:15504036
Page seeded by OCA on Thu Feb 21 15:07:36 2008
