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Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η
Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824119/ https://www.ncbi.nlm.nih.gov/pubmed/26935581 http://dx.doi.org/10.1093/nar/gkw128 |
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author | Genna, Vito Gaspari, Roberto Dal Peraro, Matteo De Vivo, Marco |
author_facet | Genna, Vito Gaspari, Roberto Dal Peraro, Matteo De Vivo, Marco |
author_sort | Genna, Vito |
collection | PubMed |
description | Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases. |
format | Online Article Text |
id | pubmed-4824119 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-48241192016-04-08 Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η Genna, Vito Gaspari, Roberto Dal Peraro, Matteo De Vivo, Marco Nucleic Acids Res Nucleic Acid Enzymes Trans-lesion synthesis polymerases, like DNA Polymerase-η (Pol-η), are essential for cell survival. Pol-η bypasses ultraviolet-induced DNA damages via a two-metal-ion mechanism that assures DNA strand elongation, with formation of the leaving group pyrophosphate (PPi). Recent structural and kinetics studies have shown that Pol-η function depends on the highly flexible and conserved Arg61 and, intriguingly, on a transient third ion resolved at the catalytic site, as lately observed in other nucleic acid-processing metalloenzymes. How these conserved structural features facilitate DNA replication, however, is still poorly understood. Through extended molecular dynamics and free energy simulations, we unravel a highly cooperative and dynamic mechanism for DNA elongation and repair, which is here described by an equilibrium ensemble of structures that connect the reactants to the products in Pol-η catalysis. We reveal that specific conformations of Arg61 help facilitate the recruitment of the incoming base and favor the proper formation of a pre-reactive complex in Pol-η for efficient DNA editing. Also, we show that a third transient metal ion, which acts concertedly with Arg61, serves as an exit shuttle for the leaving PPi. Finally, we discuss how this effective and cooperative mechanism for DNA repair may be shared by other DNA-repairing polymerases. Oxford University Press 2016-04-07 2016-03-01 /pmc/articles/PMC4824119/ /pubmed/26935581 http://dx.doi.org/10.1093/nar/gkw128 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 | Nucleic Acid Enzymes Genna, Vito Gaspari, Roberto Dal Peraro, Matteo De Vivo, Marco Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η |
title | Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η |
title_full | Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η |
title_fullStr | Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η |
title_full_unstemmed | Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η |
title_short | Cooperative motion of a key positively charged residue and metal ions for DNA replication catalyzed by human DNA Polymerase-η |
title_sort | cooperative motion of a key positively charged residue and metal ions for dna replication catalyzed by human dna polymerase-η |
topic | Nucleic Acid Enzymes |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824119/ https://www.ncbi.nlm.nih.gov/pubmed/26935581 http://dx.doi.org/10.1093/nar/gkw128 |
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