3GS8

An all-RNA hairpin ribozyme A38N1dA38 variant with a transition-state mimic substrate strand

Summary for 3GS8

• Entry DOI: 10.2210/pdb3gs8/pdb
• Related: 3GS1 3GS5
• Descriptor: RNA (5'-R(*UP*CP*CP*CP*AP*GP*UP*CP*CP*AP*CP*CP*GP*U)-3'), RNA (5'-R(*CP*GP*GP*UP*GP*AP*GP*AP*AP*GP*GP*G)-3'), RNA (5'-R(P*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, rna ribozyme, n1-deazaadenosine, rna
• Total number of polymer chains: 4
• Total formula weight: 20504.54

Authors

Spitale, R.C.,Volpini, R.,Heller, M.G.,Krucinska, J.,Cristalli, G.,Wedekind, J.E. (deposition date: 2009-03-26, release date: 2009-04-21, Last modification date: 2024-02-21)

Primary citation

Spitale, R.C.,Volpini, R.,Heller, M.G.,Krucinska, J.,Cristalli, G.,Wedekind, J.E.
Identification of an imino group indispensable for cleavage by a small ribozyme.
J.Am.Chem.Soc., 131:6093-6095, 2009

PubMed Abstract: The hairpin ribozyme is a small, noncoding RNA (ncRNA) that catalyzes a site-specific phosphodiester bond cleavage reaction. Prior biochemical and structural analyses pinpointed the amidine moiety of base Ade38 as a key functional group in catalysis, but base changes designed to probe function resulted in localized misfolding of the active site. To define the requirements for chemical activity using a conservative modification, we synthesized and incorporated N1-deazaadenosine into the full-length ribozyme construct. This single-atom variant severely impairs activity, although the active-site fold remains intact in the accompanying crystal structures. The results demonstrate the essentiality of the imino moiety as well as the importance of its interaction with the substrate in the precatalytic and transition-state conformations. This work demonstrates the efficacy of single-atom approaches in the analysis of ncRNA structure-function relationships.

PubMed: 19354216
DOI: 10.1021/ja900450h

Experimental method

X-RAY DIFFRACTION (2.85 Å)