ArticleNucleic acids research2010
Convergent donor and acceptor substrate utilization among kinase ribozymes.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 18 citations in OpenAlex.
- Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates.Nature communications · 2019Article
- Nucleobase modification by an RNA enzyme.Nucleic acids research · 2017Article
- DNA Oligonucleotide 3'-Phosphorylation by a DNA Enzyme.Biochemistry · 2016Article
- A modular tyrosine kinase deoxyribozyme with discrete aptamer and catalyst domains.Chemical communications (Cambridge, England) · 2014Article
- Lewis acid catalysis of phosphoryl transfer from a copper(II)-NTP complex in a kinase ribozyme.Nucleic acids research · 2013Article
- Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, "UCAA-motif" RNA Aptamers.Molecular therapy. Nucleic acids · 2013Article
- A small ribozyme with dual-site kinase activity.Nucleic acids research · 2012Article
- Assembly and activation of a kinase ribozyme.RNA (New York, N.Y.) · 2010Article
- Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection.PloS one · 2010Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Accommodation of donor and acceptor substrates is critical to the catalysis of (thio)phosphoryl group transfer, but there has been no systematic study of donor nucleotide recognition by kinase ribozymes, and there is relatively little known about the structural requirements for phosphorylating internal 2'OH. To address these questions, new self-phosphorylating ribozymes were selected that utilize ATP(gammaS) or GTP(gammaS) for 2'OH (thio)phosphorylation. Eight independent sequence families were identified among 57 sequenced isolates. Kinetics, donor nucleotide recognition and secondary structures were analyzed for representatives from each family. Each ribozyme was highly specific for its cognate donor. Competition assays with nucleotide analogs showed a remarkable convergence of donor recognition requirements, with critical contributions to recognition provided by the Watson-Crick face of the nucleobase, lesser contributions from donor nucleotide ribose hydroxyls, and little or no contribution from the Hoogsteen face. Importantly, most ribozymes showed evidence of significant interaction with one or more donor phosphates, suggesting that-unlike most aptamers-these ribozymes use phosphate interactions to orient the gamma phosphate within the active site for in-line displacement. All but one of the mapped (thio)phosphorylation sites are on unpaired guanosines within internal bulges. Comparative structural analysis identified three loosely-defined consensus structural motifs for kinase ribozyme active sites.
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