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| | {{STRUCTURE_2oue| PDB=2oue | SCENE= }} | | {{STRUCTURE_2oue| PDB=2oue | SCENE= }} |
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| - | '''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''
| + | ===Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution=== |
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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: Rna]] | | [[Category: Rna]] |
| | [[Category: S-turn]] | | [[Category: S-turn]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 11:40:37 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 10:43:30 2008'' |
Revision as of 07:43, 28 July 2008
Template:STRUCTURE 2oue
Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution
Template:ABSTRACT PUBMED 16411744
About this Structure
This structure supersedes the now removed PDB entry 1zfr. 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 Mon Jul 28 10:43:30 2008
