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RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution
Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group UK
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736871/ https://www.ncbi.nlm.nih.gov/pubmed/31506434 http://dx.doi.org/10.1038/s41467-019-11900-8 |
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author | Górecka, Karolina Maria Krepl, Miroslav Szlachcic, Aleksandra Poznański, Jarosław Šponer, Jiří Nowotny, Marcin |
author_facet | Górecka, Karolina Maria Krepl, Miroslav Szlachcic, Aleksandra Poznański, Jarosław Šponer, Jiří Nowotny, Marcin |
author_sort | Górecka, Karolina Maria |
collection | PubMed |
description | Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution of the HJ, the two cuts need to be tightly coordinated. They are also specific for cognate DNA sequences. Using a combination of structural biology, biochemistry, and a computational approach, here we show that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA. These changes involve rare high-energy states with protein-assisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences. These conformational changes and the relief of protein-induced structural tension of the DNA facilitate coordination between the two cuts. The unique DNA cleavage mechanism of RuvC demonstrates the importance of high-energy conformational states in nucleic acid readouts. |
format | Online Article Text |
id | pubmed-6736871 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Nature Publishing Group UK |
record_format | MEDLINE/PubMed |
spelling | pubmed-67368712019-09-12 RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution Górecka, Karolina Maria Krepl, Miroslav Szlachcic, Aleksandra Poznański, Jarosław Šponer, Jiří Nowotny, Marcin Nat Commun Article Holliday junctions (HJs) are four-way DNA structures that occur in DNA repair by homologous recombination. Specialized nucleases, termed resolvases, remove (i.e., resolve) HJs. The bacterial protein RuvC is a canonical resolvase that introduces two symmetric cuts into the HJ. For complete resolution of the HJ, the two cuts need to be tightly coordinated. They are also specific for cognate DNA sequences. Using a combination of structural biology, biochemistry, and a computational approach, here we show that correct positioning of the substrate for cleavage requires conformational changes within the bound DNA. These changes involve rare high-energy states with protein-assisted base flipping that are readily accessible for the cognate DNA sequence but not for non-cognate sequences. These conformational changes and the relief of protein-induced structural tension of the DNA facilitate coordination between the two cuts. The unique DNA cleavage mechanism of RuvC demonstrates the importance of high-energy conformational states in nucleic acid readouts. Nature Publishing Group UK 2019-09-10 /pmc/articles/PMC6736871/ /pubmed/31506434 http://dx.doi.org/10.1038/s41467-019-11900-8 Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. |
spellingShingle | Article Górecka, Karolina Maria Krepl, Miroslav Szlachcic, Aleksandra Poznański, Jarosław Šponer, Jiří Nowotny, Marcin RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution |
title | RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution |
title_full | RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution |
title_fullStr | RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution |
title_full_unstemmed | RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution |
title_short | RuvC uses dynamic probing of the Holliday junction to achieve sequence specificity and efficient resolution |
title_sort | ruvc uses dynamic probing of the holliday junction to achieve sequence specificity and efficient resolution |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6736871/ https://www.ncbi.nlm.nih.gov/pubmed/31506434 http://dx.doi.org/10.1038/s41467-019-11900-8 |
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