2oue: Difference between revisions

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[[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="350" color="white" frame="true" align="right" spinBox="true"

caption="2oue, resolution 2.05Å" />

'''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''<br />

==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.

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 [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 ~~superseeds~~ the now removed PDB entry 1ZFR. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA].

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==

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: Wedekind, J.E.]]

[[Category: Wedekind, J E.]]

[[Category: NCO]]

[[Category: SO4]]

Line 25:

[[Category: s-turn]]

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@@ Line 1: / Line 1: @@
-[[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:2oue.gif|left|200px]]<br /><applet load="2oue" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="2oue, resolution 2.05&Aring;" />
 '''Crystal structure of a junctionless all-RNA hairpin ribozyme at 2.05 angstroms resolution'''<br />
 ==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.
+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==
-OUE 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 superseeds the now removed PDB entry 1ZFR. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=2OUE OCA].
+OUE 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==
 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: Wedekind, J.E.]]
+[[Category: Wedekind, J E.]]
 [[Category: NCO]]
 [[Category: SO4]]
@@ Line 25: / Line 25: @@
 [[Category: s-turn]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 08:53:01 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 18:22:35 2008''