The structural basis of RNA-catalyzed RNA polymerization
Open accessAbstract
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.
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The crystal structure of the Class I RNA ligase suggests that this linker sequence is positioned to interact with the downstream RNA template and could strengthen the ribozyme's sequence-general contacts with the upstream duplex, enhancing primer/template binding.
“Examination of the crystal structure of the Class I RNA ligase29,30, from which the catalytic core of the ribozyme polymerase is derived, suggests this sequence is well-positioned to interact with the downstream RNA template (Fig. 3a), and could augment the sequence-general contacts the ribozyme makes with the upstream duplex16,29,31 to enhance primer/template binding.”
From In-ice evolution of RNA polymerase ribozyme activity (2013) · cites this paper as [30]
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- Authors
- Shechner, D. M., & Bartel, D. P.
- Affiliations
- Whitehead Institute for Biomedical Research (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Bartel, David P
- Venue
- Nature Structural & Molecular Biology
- Published
- 2011-08-21
- Volume
- 18
- Issue
- 9
- Pages
- 1036-1042
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC3169305
- OpenAlex
- W1589907089
- Cited by
- 48
- References
- 57
- Citations by year
- 2026: 4 · 2025: 2 · 2024: 4 · 2023: 4 · 2021: 3 · 2020: 4 · 2019: 5 · 2018: 3 · 2017: 2 · 2016: 4 · 2015: 3 · 2014: 4 · 2013: 5 · 2012: 1
- FWCI
- 1.30
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Structural & Molecular Biology (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
- DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc-sa)
- PMC
- Funders
- Howard Hughes Medical Institute
- National Institute of General Medical Sciences (GM061835, R01GM061835, R37GM061835)
- National Center for Research Resources (RR 15301, P41RR015301)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Physical Sciences › Physics and Astronomy › Astronomy and Astrophysics › Origins and Evolution of Life
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
- Keywords
- RNA polymerization, ribozymes, RNA ligase, RNA replication, RNA world, crystal structure, catalytic mechanism, active site metal ions, nucleophilic attack, 5'-triphosphate, early life, mutagenesis
- MeSH terms
- Models, Molecular, Nucleic Acid Conformation, Polyphosphates, RNA, RNA, Catalytic, Crystallography, X-Ray, Catalytic Domain, Static Electricity, Polymerization
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
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