PDBsum entry 2bcz

RNA

PDB id: 2bcz

Contents

DNA/RNA

Ligands

SO4

NCO ×2

Waters ×5

PDB id:

2bcz

Name:

RNA

Title:

Crystal structure of a minimal, mutant all-RNA hairpin ribozyme (u39c, g8i, 2'deoxy a-1)

Structure:

5'-r( Up Cp Cp Cp (Da)p Gp Up Cp Cp Ap Cp Cp G)-3'). Chain: a. Engineered: yes. Mutation: yes. 5'-r( Cp Gp Gp Up Gp Ap Ip Ap Ap Gp Gp G)-3'. Chain: b. Engineered: yes. Mutation: yes. 5'-r( Gp Gp Cp Ap Gp Ap Gp Ap Ap Ap Cp Ap Cp Ap Cp Gp A)-

Source:

Synthetic: yes. Synthetic: yes

Biol. unit:

Tetramer (from PQS)

Resolution:

2.40Å R-factor: 0.240 R-free: 0.270

Authors:

J.D.Salter,J.E.Wedekind

Key ref:

J.Salter et al. (2006). 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. PubMed id: 16411744 DOI: 10.1021/bi051887k

Date:

19-Oct-05 Release date: 14-Feb-06

DNA/RNA chains

U-C-C-C-A-G-U-C-C-A-C-C-G 13 bases

C-G-G-U-G-A-I-A-A-G-G-G 12 bases

G-G-C-A-G-A-G-A-A-A-C-A-C-A-C-G-A 17 bases

U-C-G-U-G-G-U-A-C-A-U-U-A-C-C-U-G-C-C 19 bases

DOI no: 10.1021/bi051887k

Biochemistry 45:686-700 (2006)

PubMed id: 16411744

Water in the active site of an all-RNA hairpin ribozyme and effects of Gua8 base variants on the geometry of phosphoryl transfer.

J.Salter, J.Krucinska, S.Alam, V.Grum-Tokars, J.E.Wedekind.

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.