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| | {{STRUCTURE_1zfv| PDB=1zfv | SCENE= }} | | {{STRUCTURE_1zfv| PDB=1zfv | SCENE= }} |
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| - | '''The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site'''
| + | ===The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site=== |
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| - | ==Overview==
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| - | The hairpin ribozyme requires functional group contributions from G8 to assist in phosphodiester bond cleavage. Previously, replacement of G8 by a series of nucleobase variants showed little effect on interdomain docking, but a 3-250-fold effect on catalysis. To identify G8 features that contribute to catalysis within the hairpin ribozyme active site, structures for five base variants were determined by X-ray crystallography in a resolution range between 2.3 and 2.7 A. For comparison, a native all-RNA "G8" hairpin ribozyme structure was refined to 2.05 A resolution. The native structure revealed a scissile bond angle (tau) of 158 degrees, which is close to the requisite 180 degrees "in-line" geometry. Mutations G8(inosine), G8(diaminopurine), G8(aminopurine), G8(adenosine), and G8(uridine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees to 93 degrees) that paralleled their diminished solution activities. A superposition ensemble of all structures, including a previously described hairpin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resulting from perturbation of the chemical environment and provided a rationale for how the exocyclic amine of nucleobase 8 promotes productive, in-line geometry. Changes at position 8 also caused variations in the A-1 sugar pucker. In this regard, variants A8 and U8 appeared to represent nonproductive ground states in which their 2'-OH groups mimicked the pro-R, nonbridging oxygen of the vanadate transition-state complex. Finally, the results indicated that ordered water molecules bind near the 2'-hydroxyl of A-1, lending support to the hypothesis that solvent may play an important role in the reaction. | + | The line below this paragraph, {{ABSTRACT_PUBMED_16411744}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 16411744 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_16411744}} |
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| | ==About this Structure== | | ==About this Structure== |
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| | [[Category: Ribose zipper]] | | [[Category: Ribose zipper]] |
| | [[Category: S-turn]] | | [[Category: S-turn]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:34:23 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:32:21 2008'' |
Revision as of 10:32, 29 July 2008
Template:STRUCTURE 1zfv
The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site
Template:ABSTRACT PUBMED 16411744
About this Structure
Full crystallographic information is available from OCA.
Reference
Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer., Salter J, Krucinska J, Alam S, Grum-Tokars V, Wedekind JE, Biochemistry. 2006 Jan 24;45(3):686-700. PMID:16411744
Page seeded by OCA on Tue Jul 29 13:32:21 2008
