PDBsum entry 3i2s

RNA

PDB id: 3i2s

Contents

DNA/RNA

Ligands

SO4

NCO ×2

PDB id:

3i2s

Name:

RNA

Title:

Crystal structure of the hairpin ribozyme with a 2'ome substrate and n1-deazaadenosine at position a10

Structure:

5'-r( Up Cp Cp Cp (A2m)p Gp Up Cp Cp Ap Cp Cp Gp U)-3'. Chain: a. Engineered: yes. Other_details: hairpin ribozyme. DNA/RNA (30-mer). Chain: b. Engineered: yes. Other_details: hairpin ribozyme. 5'-r( Up Cp Gp Up Gp Gp Up Ap Cp Ap Up Up Ap Cp Cp Up Gp Cp

Source:

Synthetic: yes. Other_details: the RNA was synthesized by dharmacon inc., Following the tobacco ringspot virus sequence. The tobacco ringspot virus sequence

Resolution:

2.75Å R-factor: 0.239 R-free: 0.261

Authors:

J.E.Wedekind,R.C.Spitale,J.Krucinska

Key ref:

R.C.Spitale et al. (2009). Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core. Biochemistry, 48, 7777-7779. PubMed id: 19634899

Date:

29-Jun-09 Release date: 03-Nov-09

DNA/RNA chains

U-C-C-C-A2M-G-U-C-C-A-C-C-G 13 bases

C-G-G-U-G-A-G-A-1DP-G-G-G-S9L-G-G-C-A-G-A-G-A-A-A-C-A-C-A-C-G-A 30 bases

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

Biochemistry 48:7777-7779 (2009)

PubMed id: 19634899

Single-atom imino substitutions at A9 and A10 reveal distinct effects on the fold and function of the hairpin ribozyme catalytic core.

R.C.Spitale, R.Volpini, M.V.Mungillo, J.Krucinska, G.Cristalli, J.E.Wedekind.

ABSTRACT

The hairpin ribozyme cleaves a phosphodiester bond within a cognate substrate. Structural and biochemical data indicate the conserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalysis. To investigate these residues, we replaced the imino moiety of each base with N1-deazaadenosine. This single-atom change resulted in an 8-fold loss in k(obs) for A9 and displacement of the base from the active site; no effects were observed for A10. We propose that the imino moiety of A9 promotes a key water-mediated contact that favors transition-state formation, which suggests an enhanced chemical repertoire for RNA.