2oue
From Proteopedia
(New page: 200px<br /><applet load="2oue" size="450" color="white" frame="true" align="right" spinBox="true" caption="2oue, resolution 2.05Å" /> '''Crystal structure of...) |
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| - | [[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size=" | + | [[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="350" color="white" frame="true" align="right" spinBox="true" |
caption="2oue, resolution 2.05Å" /> | caption="2oue, resolution 2.05Å" /> | ||
'''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''<br /> | '''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''<br /> | ||
==Overview== | ==Overview== | ||
| - | The hairpin ribozyme requires functional group contributions from G8 to | + | 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. |
==About this Structure== | ==About this Structure== | ||
| - | 2OUE is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with SO4 and NCO as [http://en.wikipedia.org/wiki/ligands ligands]. This structure | + | 2OUE is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SO4:'>SO4</scene> and <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligands ligands]. This structure supersedes the now removed PDB entry 1ZFR. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA]. |
==Reference== | ==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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16411744 16411744] | 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:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=16411744 16411744] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
| - | [[Category: Wedekind, J | + | [[Category: Wedekind, J E.]] |
[[Category: NCO]] | [[Category: NCO]] | ||
[[Category: SO4]] | [[Category: SO4]] | ||
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[[Category: s-turn]] | [[Category: s-turn]] | ||
| - | ''Page seeded by [http:// | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:22:35 2008'' |
Revision as of 16:22, 21 February 2008
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Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution
Overview
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.
About this Structure
2OUE is a Protein complex structure of sequences from [1] with and as ligands. 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 Thu Feb 21 18:22:35 2008
Categories: Protein complex | Wedekind, J E. | NCO | SO4 | All-rna | Catalytic rna | E-loop | Hairpin ribozyme | Low salt | Mutation | Ribose zipper | Rna | S-turn
