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DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target

R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calci...

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Autores principales: Shen, Betty W., Heiter, Daniel F., Lunnen, Keith D., Wilson, Geoffrey G., Stoddard, Barry L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5415892/
https://www.ncbi.nlm.nih.gov/pubmed/28180307
http://dx.doi.org/10.1093/nar/gkw1200
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author Shen, Betty W.
Heiter, Daniel F.
Lunnen, Keith D.
Wilson, Geoffrey G.
Stoddard, Barry L.
author_facet Shen, Betty W.
Heiter, Daniel F.
Lunnen, Keith D.
Wilson, Geoffrey G.
Stoddard, Barry L.
author_sort Shen, Betty W.
collection PubMed
description R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar ‘PD-D/ExK’ restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs. Binding by SwaI induces an extreme bend in the target sequence accompanied by un-pairing and re-ordering of its central A:T base pairs. This result is reminiscent of a more dramatic target deformation previously described for PacI, implying that long A:T-rich target sites might display structural or dynamic behaviors that play a significant role in endonuclease recognition and cleavage.
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spelling pubmed-54158922017-05-05 DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target Shen, Betty W. Heiter, Daniel F. Lunnen, Keith D. Wilson, Geoffrey G. Stoddard, Barry L. Nucleic Acids Res Structural Biology R.SwaI, a Type IIP restriction endonuclease, recognizes a palindromic eight base pair (bp) symmetric sequence, 5΄-ATTTAAAT-3΄, and cleaves that target at its center to generate blunt-ended DNA fragments. Here, we report three crystal structures of SwaI: unbound enzyme, a DNA-bound complex with calcium ions; and a DNA-bound, fully cleaved complex with magnesium ions. We compare these structures to two structurally similar ‘PD-D/ExK’ restriction endonucleases (EcoRV and HincII) that also generate blunt-ended products, and to a structurally distinct enzyme (the HNH endonuclease PacI) that also recognizes an 8-bp target site consisting solely of A:T base pairs. Binding by SwaI induces an extreme bend in the target sequence accompanied by un-pairing and re-ordering of its central A:T base pairs. This result is reminiscent of a more dramatic target deformation previously described for PacI, implying that long A:T-rich target sites might display structural or dynamic behaviors that play a significant role in endonuclease recognition and cleavage. Oxford University Press 2017-02-17 2016-11-29 /pmc/articles/PMC5415892/ /pubmed/28180307 http://dx.doi.org/10.1093/nar/gkw1200 Text en © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Structural Biology
Shen, Betty W.
Heiter, Daniel F.
Lunnen, Keith D.
Wilson, Geoffrey G.
Stoddard, Barry L.
DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target
title DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target
title_full DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target
title_fullStr DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target
title_full_unstemmed DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target
title_short DNA recognition by the SwaI restriction endonuclease involves unusual distortion of an 8 base pair A:T-rich target
title_sort dna recognition by the swai restriction endonuclease involves unusual distortion of an 8 base pair a:t-rich target
topic Structural Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5415892/
https://www.ncbi.nlm.nih.gov/pubmed/28180307
http://dx.doi.org/10.1093/nar/gkw1200
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