3R1H

Crystal structure of the Class I ligase ribozyme-substrate preligation complex, C47U mutant, Ca2+ bound

Summary for 3R1H

• Entry DOI: 10.2210/pdb3r1h/pdb
• Related: 3HHN 3IVK 3R1L
• Descriptor: U1 small nuclear ribonucleoprotein A, 5'-R(*UP*CP*CP*AP*GP*UP*A)-3', Class I ligase ribozyme, ... (5 entities in total)
• Functional Keywords: ligase ribozyme, catalytic rna, ribozyme, rna binding protein-rna complex, rna binding protein/rna
• Biological source: Homo sapiens (human); More
• Cellular location: Nucleus: P09012
• Total number of polymer chains: 6
• Total formula weight: 112291.18

Authors

Shechner, D.M.,Bartel, D.P. (deposition date: 2011-03-10, release date: 2011-08-31, Last modification date: 2023-09-13)

Primary citation

Shechner, D.M.,Bartel, D.P.
The structural basis of RNA-catalyzed RNA polymerization.
Nat.Struct.Mol.Biol., 18:1036-1042, 2011

PubMed 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.

PubMed: 21857665
DOI: 10.1038/nsmb.2107

Experimental method

X-RAY DIFFRACTION (3.15 Å)