1ZFX

The Structure of a minimal all-RNA Hairpin Ribozyme with the mutant G8U at the cleavage site

Summary for 1ZFX

• Entry DOI: 10.2210/pdb1zfx/pdb
• Related: 1X9C 1X9K 1ZFR 1ZFT 1ZFV
• Descriptor: 5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*G)-3', 5'-R(*CP*GP*GP*UP*GP*AP*UP*AP*AP*GP*GP*G)-3', 5'-R(*GP*GP*CP*AP*GP*AP*GP*AP*AP*AP*CP*AP*CP*AP*CP*GP*A)-3', ... (7 entities in total)
• Functional Keywords: hairpin ribozyme, all-rna, cobalt hexaamine, mutation, low salt, s-turn, e-loop, ribose zipper, catalytic rna, rna
• Total number of polymer chains: 4
• Total formula weight: 19929.19

Authors

Wedekind, J.E. (deposition date: 2005-04-20, release date: 2006-02-14, Last modification date: 2023-08-23)

Primary citation

Salter, J.,Krucinska, J.,Alam, S.,Grum-Tokars, V.,Wedekind, J.E.
Water in the Active Site of an All-RNA Hairpin Ribozyme and Effects of Gua8 Base Variants on the Geometry of Phosphoryl Transfer.
Biochemistry, 45:686-700, 2006

PubMed Abstract: 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.

PubMed: 16411744
DOI: 10.1021/bi051887k

Experimental method

X-RAY DIFFRACTION (2.38 Å)