ArticleNature structural & molecular biology2015
Visualizing phosphodiester-bond hydrolysis by an endonuclease.
Article in Nature structural & molecular biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 31 citations in OpenAlex.
- New insights into DNA polymerase mechanisms provided by time-lapse crystallography.Current opinion in structural biology · 2022Review
- Visualizing the three-metal-ion-dependent cleavage of a mutagenic nucleotide.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Visualization of mutagenic nucleotide processing byProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Recruiting Mechanism and Functional Role of a Third Metal Ion in the Enzymatic Activity of 5' Structure-Specific Nucleases.Journal of the American Chemical Society · 2020Article
- Intrinsic Cleavage of RNA Polymerase II Adopts a Nucleobase-independent Mechanism Assisted by Transcript Phosphate.Nature catalysis · 2019Article
- Dynamic coordination of two-metal-ions orchestrates λ-exonuclease catalysis.Nature communications · 2018Article
- Understanding the indirect DNA read-out specificity of I-CreI Meganuclease.Scientific reports · 2018Article
- Second-Shell Basic Residues Expand the Two-Metal-Ion Architecture of DNA and RNA Processing Enzymes.Structure (London, England : 1993) · 2018Article
- Structure and dynamics of mesophilic variants from the homing endonuclease I-DmoI.Journal of computer-aided molecular design · 2017Article
- Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing.Nature structural & molecular biology · 2017Review
- Phosphate steering by Flap Endonuclease 1 promotes 5'-flap specificity and incision to prevent genome instability.Nature communications · 2017Article
- Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions.Acta crystallographica. Section F, Structural biology communications · 2016Article
- Crystal Structure of the Homing Endonuclease I-CvuI Provides a New Template for Genome Modification.The Journal of biological chemistry · 2015Article
- A comparative interplay between small heterorings and hypofluorous acids.Journal of molecular modeling · 2015Article
- Capturing snapshots of APE1 processing DNA damage.Nature structural & molecular biology · 2015Article
- Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold.The Journal of biological chemistry · 2015Article
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Authors and funding
8 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The enzymatic hydrolysis of DNA phosphodiester bonds has been widely studied, but the chemical reaction has not yet been observed. Here we follow the generation of a DNA double-strand break (DSB) by the Desulfurococcus mobilis homing endonuclease I-DmoI, trapping sequential stages of a two-metal-ion cleavage mechanism. We captured intermediates of the different catalytic steps, and this allowed us to watch the reaction by 'freezing' multiple states. We observed the successive entry of two metals involved in the reaction and the arrival of a third cation in a central position of the active site. This third metal ion has a crucial role, triggering the consecutive hydrolysis of the targeted phosphodiester bonds in the DNA strands and leaving its position once the DSB is generated. The multiple structures show the orchestrated conformational changes in the protein residues, nucleotides and metals during catalysis.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.