title: The structural basis of RNA-catalyzed RNA polymerization.
abstract: 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.
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.
authors.forename: David M
authors.initials: DM
authors.lastname: Shechner
authors.forename: David P
authors.initials: DP
authors.lastname: Bartel
mesh_terms: D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D058105:Polymerization; D011122:Polyphosphates / Q000737:chemistry; D012313:RNA / Q000378:metabolism*; D016337:RNA, Catalytic / Q000737:chemistry* / Q000502:physiology; D055672:Static Electricity
chemical_list: D011122:Polyphosphates; D016337:RNA, Catalytic; D012313:RNA; C005692:triphosphoric acid