The structural basis of RNA-catalyzed RNA polymerization.
Publication Type:Journal Article
Source:Nat Struct Mol Biol, Volume 18, Issue 9, p.1036-42 (2011)
Keywords:Catalytic Domain, Crystallography, X-Ray, Models, Molecular, Nucleic Acid Conformation, Polymerization, Polyphosphates, RNA, RNA, Catalytic, Static Electricity
<p>Early life presumably required polymerase ribozymes capable of replicating RNA. Known polymerase ribozymes best approximating such replicases use as their catalytic engine an RNA-ligase ribozyme originally selected from random RNA sequences. Here we report 3.15-Å crystal structures of this ligase trapped in catalytically viable preligation states, with the 3'-hydroxyl nucleophile positioned for in-line attack on the 5'-triphosphate. Guided by metal- and solvent-mediated interactions, the 5'-triphosphate hooks into the major groove of the adjoining RNA duplex in an unanticipated conformation. Two phosphates and the nucleophile jointly coordinate an active-site metal ion. Atomic mutagenesis experiments demonstrate that active-site nucleobase and hydroxyl groups also participate directly in catalysis, collectively playing a role that in proteinaceous polymerases is performed by a second metal ion. Thus artificial ribozymes can use complex catalytic strategies that differ markedly from those of analogous biological enzymes.</p>