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1syz

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[[Image:1syz.gif|left|200px]]
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{{Seed}}
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{{STRUCTURE_1syz| PDB=1syz | SCENE= }}
{{STRUCTURE_1syz| PDB=1syz | SCENE= }}
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'''Solution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7'''
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===Solution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7===
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==Overview==
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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.
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(as it appears on PubMed at http://www.pubmed.gov), where 15504036 is the PubMed ID number.
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{{ABSTRACT_PUBMED_15504036}}
==About this Structure==
==About this Structure==
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SYZ OCA].
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1SYZ OCA].
==Reference==
==Reference==
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[[Category: Rna]]
[[Category: Rna]]
[[Category: Stem-loop]]
[[Category: Stem-loop]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 09:17:46 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 14:32:38 2008''

Revision as of 11:32, 29 July 2008

Image:1syz.png

Template:STRUCTURE 1syz

Solution structure of the S. Cerevisiae U6 intramolecular stem loop (ISL) RNA at pH 5.7

Template:ABSTRACT PUBMED 15504036

About this Structure

Full experimental 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 Tue Jul 29 14:32:38 2008

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