1zfv

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[[Image:1zfv.gif|left|200px]]
[[Image:1zfv.gif|left|200px]]
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{{Structure
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|PDB= 1zfv |SIZE=350|CAPTION= <scene name='initialview01'>1zfv</scene>, resolution 2.40&Aring;
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The line below this paragraph, containing "STRUCTURE_1zfv", creates the "Structure Box" on the page.
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|SITE=
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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|LIGAND= <scene name='pdbligand=A:ADENOSINE-5&#39;-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=C:CYTIDINE-5&#39;-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5&#39;-MONOPHOSPHATE'>G</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=U:URIDINE-5&#39;-MONOPHOSPHATE'>U</scene>
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|DOMAIN=
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{{STRUCTURE_1zfv| PDB=1zfv | SCENE= }}
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|RELATEDENTRY=[[1x9c|1X9C]], [[1x9k|1X9K]], [[1zfr|1ZFR]], [[1zft|1ZFT]], [[1zfx|1ZFX]]
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1zfv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1zfv OCA], [http://www.ebi.ac.uk/pdbsum/1zfv PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1zfv RCSB]</span>
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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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==About this Structure==
==About this Structure==
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1ZFV is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFV OCA].
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ZFV 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://www.ncbi.nlm.nih.gov/pubmed/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://www.ncbi.nlm.nih.gov/pubmed/16411744 16411744]
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[[Category: Protein complex]]
 
[[Category: Wedekind, J E.]]
[[Category: Wedekind, J E.]]
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[[Category: all-rna]]
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[[Category: All-rna]]
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[[Category: catalytic rna]]
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[[Category: Catalytic rna]]
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[[Category: cobalt hexaamine]]
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[[Category: Cobalt hexaamine]]
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[[Category: e-loop]]
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[[Category: E-loop]]
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[[Category: hairpin ribozyme]]
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[[Category: Hairpin ribozyme]]
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[[Category: junctionless]]
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[[Category: Junctionless]]
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[[Category: low salt]]
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[[Category: Low salt]]
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[[Category: mutation]]
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[[Category: Mutation]]
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[[Category: ribose zipper]]
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[[Category: Ribose zipper]]
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[[Category: s-turn]]
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[[Category: S-turn]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 17:34:23 2008''
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 01:35:28 2008''
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Revision as of 14:34, 3 May 2008

Image:1zfv.gif

Template:STRUCTURE 1zfv

The structure of an all-RNA minimal Hairpin Ribozyme with Mutation G8A at the cleavage site


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

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 Sat May 3 17:34:23 2008

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