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Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation
Restriction endonucleases naturally target DNA duplexes. Systematic screening has identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes and that may therefore be useful as tools for RNA biochemistry. We have chosen AvaII (G↓GWCC, where W stands for A or T) as a rep...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Oxford University Press
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337904/ https://www.ncbi.nlm.nih.gov/pubmed/32459314 http://dx.doi.org/10.1093/nar/gkaa403 |
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author | Kisiala, Marlena Kowalska, Monika Pastor, Michal Korza, Henryk J Czapinska, Honorata Bochtler, Matthias |
author_facet | Kisiala, Marlena Kowalska, Monika Pastor, Michal Korza, Henryk J Czapinska, Honorata Bochtler, Matthias |
author_sort | Kisiala, Marlena |
collection | PubMed |
description | Restriction endonucleases naturally target DNA duplexes. Systematic screening has identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes and that may therefore be useful as tools for RNA biochemistry. We have chosen AvaII (G↓GWCC, where W stands for A or T) as a representative of this group of restriction endonucleases for detailed characterization. Here, we report crystal structures of AvaII alone, in specific complex with partially cleaved dsDNA, and in scanning complex with an RNA/DNA hybrid. The specific complex reveals a novel form of semi-specific dsDNA readout by a hexa-coordinated metal cation, most likely Ca(2+) or Mg(2+). Substitutions of residues anchoring this non-catalytic metal ion severely impair DNA binding and cleavage. The dsDNA in the AvaII complex is in the A-like form. This creates space for 2′-OH groups to be accommodated without intra-nucleic acid steric conflicts. PD-(D/E)XK restriction endonucleases of known structure that bind their dsDNA targets in the A-like form cluster into structurally similar groups. Most such enzymes, including some not previously studied in this respect, cleave RNA/DNA heteroduplexes. We conclude that A-form dsDNA binding is a good predictor for RNA/DNA cleavage activity. |
format | Online Article Text |
id | pubmed-7337904 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-73379042020-07-13 Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation Kisiala, Marlena Kowalska, Monika Pastor, Michal Korza, Henryk J Czapinska, Honorata Bochtler, Matthias Nucleic Acids Res Structural Biology Restriction endonucleases naturally target DNA duplexes. Systematic screening has identified a small minority of these enzymes that can also cleave RNA/DNA heteroduplexes and that may therefore be useful as tools for RNA biochemistry. We have chosen AvaII (G↓GWCC, where W stands for A or T) as a representative of this group of restriction endonucleases for detailed characterization. Here, we report crystal structures of AvaII alone, in specific complex with partially cleaved dsDNA, and in scanning complex with an RNA/DNA hybrid. The specific complex reveals a novel form of semi-specific dsDNA readout by a hexa-coordinated metal cation, most likely Ca(2+) or Mg(2+). Substitutions of residues anchoring this non-catalytic metal ion severely impair DNA binding and cleavage. The dsDNA in the AvaII complex is in the A-like form. This creates space for 2′-OH groups to be accommodated without intra-nucleic acid steric conflicts. PD-(D/E)XK restriction endonucleases of known structure that bind their dsDNA targets in the A-like form cluster into structurally similar groups. Most such enzymes, including some not previously studied in this respect, cleave RNA/DNA heteroduplexes. We conclude that A-form dsDNA binding is a good predictor for RNA/DNA cleavage activity. Oxford University Press 2020-07-09 2020-05-27 /pmc/articles/PMC7337904/ /pubmed/32459314 http://dx.doi.org/10.1093/nar/gkaa403 Text en © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Structural Biology Kisiala, Marlena Kowalska, Monika Pastor, Michal Korza, Henryk J Czapinska, Honorata Bochtler, Matthias Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation |
title | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation |
title_full | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation |
title_fullStr | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation |
title_full_unstemmed | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation |
title_short | Restriction endonucleases that cleave RNA/DNA heteroduplexes bind dsDNA in A-like conformation |
title_sort | restriction endonucleases that cleave rna/dna heteroduplexes bind dsdna in a-like conformation |
topic | Structural Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7337904/ https://www.ncbi.nlm.nih.gov/pubmed/32459314 http://dx.doi.org/10.1093/nar/gkaa403 |
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