3I2S

Crystal structure of the hairpin ribozyme with a 2'OMe substrate and N1-deazaadenosine at position A10

Summary for 3I2S

• Entry DOI: 10.2210/pdb3i2s/pdb
• Related: 3I2P 3I2Q 3I2R 3I2U
• Descriptor: 5'-R(*UP*CP*CP*CP*(A2M)P*GP*UP*CP*CP*AP*CP*CP*GP*U)-3', DNA/RNA (30-MER), 5'-R(*UP*CP*GP*UP*GP*GP*UP*AP*CP*AP*UP*UP*AP*CP*CP*UP*GP*CP*C)-3', ... (5 entities in total)
• Functional Keywords: hairpin ribozyme, n1-deazaadenosine, rna
• Total number of polymer chains: 3
• Total formula weight: 20544.53

Authors

Wedekind, J.E.,Spitale, R.C.,Krucinska, J. (deposition date: 2009-06-29, release date: 2009-11-03, Last modification date: 2023-09-06)

Primary citation

Spitale, R.C.,Volpini, R.,Mungillo, M.V.,Krucinska, J.,Cristalli, G.,Wedekind, J.E.
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, 2009

PubMed 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.

PubMed: 19634899
DOI: 10.1021/bi9011622

Experimental method

X-RAY DIFFRACTION (2.75 Å)