2bcy: Difference between revisions
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'''Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)''' | {{Structure | ||
|PDB= 2bcy |SIZE=350|CAPTION= <scene name='initialview01'>2bcy</scene>, resolution 2.70Å | |||
|SITE= | |||
|LIGAND= <scene name='pdbligand=NCO:COBALT HEXAMMINE ION'>NCO</scene> | |||
|ACTIVITY= | |||
|GENE= | |||
}} | |||
'''Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)''' | |||
==Overview== | ==Overview== | ||
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==About this Structure== | ==About this Structure== | ||
2BCY is a [ | 2BCY 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=2BCY 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:// | 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] | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Salter, J D.]] | [[Category: Salter, J D.]] | ||
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[[Category: ribozyme]] | [[Category: ribozyme]] | ||
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 16:00:18 2008'' | ||
Revision as of 14:00, 20 March 2008
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| 2bcy, resolution 2.70Å | |||||||||||||
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| Ligands: | NCO | ||||||||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||||||||
Crystal Structure of a minimal, mutant all-RNA hairpin ribozyme (U39C, G8MTU)
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
2BCY is a Protein complex structure of sequences from [1]. 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
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