2oue
From Proteopedia
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|PDB= 2oue |SIZE=350|CAPTION= <scene name='initialview01'>2oue</scene>, resolution 2.05Å | |PDB= 2oue |SIZE=350|CAPTION= <scene name='initialview01'>2oue</scene>, resolution 2.05Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand= | + | |LIGAND= <scene name='pdbligand=A:ADENOSINE-5'-MONOPHOSPHATE'>A</scene>, <scene name='pdbligand=A2M:2'-O-METHYL-ADENOSINE-5'-MONOPHOSPHATE'>A2M</scene>, <scene name='pdbligand=C:CYTIDINE-5'-MONOPHOSPHATE'>C</scene>, <scene name='pdbligand=G:GUANOSINE-5'-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'-MONOPHOSPHATE'>U</scene> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY=[[1zfx|1ZFX]], [[1zfv|1ZFV]], [[1zft|1ZFT]], [[2bcy|2BCY]], [[2fgp|2FGP]], [[2bcz|2BCZ]], [[1x9k|1X9K]], [[1x9c|1X9C]] | ||
| + | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2oue FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2oue OCA], [http://www.ebi.ac.uk/pdbsum/2oue PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=2oue RCSB]</span> | ||
}} | }} | ||
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[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Wedekind, J E.]] | [[Category: Wedekind, J E.]] | ||
| - | [[Category: NCO]] | ||
| - | [[Category: SO4]] | ||
[[Category: all-rna]] | [[Category: all-rna]] | ||
[[Category: catalytic rna]] | [[Category: catalytic rna]] | ||
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[[Category: s-turn]] | [[Category: s-turn]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Mar 31 04:23:13 2008'' |
Revision as of 01:23, 31 March 2008
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| , resolution 2.05Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , , , | ||||||
| Related: | 1ZFX, 1ZFV, 1ZFT, 2BCY, 2FGP, 2BCZ, 1X9K, 1X9C
| ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
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]. 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 Mar 31 04:23:13 2008
Categories: Protein complex | Wedekind, J E. | All-rna | Catalytic rna | E-loop | Hairpin ribozyme | Low salt | Mutation | Ribose zipper | Rna | S-turn
