The Structural Basis of Ribozyme-Catalyzed RNA Assembly
Open accessAbstract
Life originated, according to the RNA World hypothesis, from self-replicating ribozymes that catalyzed ligation of RNA fragments. We have solved the 2.6 angstrom crystal structure of a ligase ribozyme that catalyzes regiospecific formation of a 5' to 3' phosphodiester bond between the 5'-triphosphate and the 3'-hydroxyl termini of two RNA fragments. Invariant residues form tertiary contacts that stabilize a flexible stem of the ribozyme at the ligation site, where an essential magnesium ion coordinates three phosphates. The structure of the active site permits us to suggest how transition-state stabilization and a general base may catalyze the ligation reaction required for prebiotic RNA assembly.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The L1 structure shows a bound metal ion in the active site, coordinated by three nonbridging phosphate oxygens, one of which belongs to the newly formed phosphodiester linkage.
“The L1 structure (Fig. 6A) shows a bound metal ion in the active site, coordinated by three nonbridging phosphate oxygens, one of which belongs to the newly formed phosphodiester linkage.”
From Protocells and RNA Self-Replication (2018) · cites this paper as Robertson and Scott 2007
Both the L1 and class I ligases are dependent on Mg2+ ions for their activity.
“Both ligases are dependent on Mg 2+ ions for their activity.”
From Protocells and RNA Self-Replication (2018) · cites this paper as Robertson and Scott 2007
RNA polymerase enzymes solve the problems of metal ion catalysis by binding and precisely positioning the metal ion for catalysis.
“RNA polymerase enzymes solve these problems by binding and precisely positioning the metal ion for catalysis (Zhang et al. 1999;Cramer et al. 2001;Robertson and Scott 2007;Shechner et al. 2009).”
From Protocells and RNA Self-Replication (2018) · cites this paper as Robertson and Scott 2007
Cites
The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme
Guerrier-Takada, C., Gardiner, K., Marsh, T., Pace, N., & Altman, S. (1983) · Cell · doi:10.1016/0092-8674(83)90117-4 · Cited by 2,684 · see citing works
Isolation of New Ribozymes from a Large Pool of Random Sequences
Bartel, D. P., & Szostak, J. W. (1993) · Science · doi:10.1126/science.7690155 · Cited by 900 · see citing works
RNA-catalyzed RNA polymerization: Accurate and general RNA-templated primer extension.
Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., & Bartel, D. P. (2001) · Science · doi:10.1126/science.1060786 · Cited by 768 · see citing works
The chemical repertoire of natural ribozymes
Doudna, J. A., & Cech, T. R. (2002) · Nature · doi:10.1038/418222a · Cited by 745 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Robertson, M. P., & Joyce, G. F. (2012) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a003608 · Cited by 556 · see citing works
Self-citationProtocells and RNA Self-Replication
Joyce, G. F., & Szostak, J. W. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a034801 · Cited by 308 · see citing works
Crystal Structure of the Catalytic Core of an RNA-Polymerase Ribozyme
Shechner, D. M., Grant, R. A., Bagby, S. C., Koldobskaya, Y., Piccirilli, J. A., & Bartel, D. P. (2009) · Science · doi:10.1126/science.1174676 · Cited by 136 · see citing works
The dawn of the RNA World: toward functional complexity through ligation of random RNA oligomers
Briones, C., Stich, M., & Manrubia, S. C. (2009) · RNA · doi:10.1261/rna.1488609 · Cited by 114 · see citing works
Closing the circle: replicating RNA with RNA.
Cheng, L. K. L., & Unrau, P. J. (2010) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a002204 · Cited by 58 · see citing works
Chiral encoding may provide a simple solution to the origin of life
Brewer, A., & Davis, A. P. (2014) · Nature Chemistry · doi:10.1038/nchem.1981 · Cited by 51 · see citing works
The structural basis of RNA-catalyzed RNA polymerization
Shechner, D. M., & Bartel, D. P. (2011) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2107 · Cited by 48 · see citing works
Bit by bit: The Darwinian basis of life
Joyce, G. F. (2012) · PLoS Biology · doi:10.1371/journal.pbio.1001323 · Cited by 45 · see citing works
Lower temperature optimum of a smaller, fragmented triphosphorylation ribozyme
Akoopie, A., & Müller, U. F. (2016) · Physical Chemistry Chemical Physics · doi:10.1039/c6cp00672h · Cited by 16 · see citing works
- Authors
- Robertson, M. P., & Scott, W. G.
- Affiliations
- University of California, Santa Cruz (US)
- Corresponding author
- Scott, William G.
- Venue
- Science
- Published
- 2007-03-16
- Volume
- 315
- Issue
- 5818
- Pages
- 1549-1553
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2080284797
- Cited by
- 111
- References
- 4
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 3 · 2023: 3 · 2022: 2 · 2021: 1 · 2020: 4 · 2019: 5 · 2018: 6 · 2017: 5 · 2016: 3 · 2015: 5 · 2014: 7 · 2013: 2 · 2012: 10
- FWCI
- 5.44
- Type
- journal article
- Language
- en
- Open access
- green
- escholarship.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- National Institute of General Medical Sciences (R01GM087721)
- 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
- ribozymes, RNA ligase, RNA ligation, RNA world, phosphodiester bond formation, crystal structure, magnesium coordination, active site, transition state stabilization, general base catalysis, RNA tertiary structure
- MeSH terms
- Binding Sites, Catalysis, Crystallization, Hydrogen Bonding, Models, Molecular, Molecular Conformation, Nucleic Acid Conformation, Oligoribonucleotides, Ribonucleotides, Templates, Genetic, RNA, Catalytic, Crystallography, X-Ray, Directed Molecular Evolution, Base Pairing, Catalytic Domain
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.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
