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A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase
In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in...
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/PMC4737139/ https://www.ncbi.nlm.nih.gov/pubmed/26553802 http://dx.doi.org/10.1093/nar/gkv1092 |
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author | Li, Haoquan Endutkin, Anton V. Bergonzo, Christina Campbell, Arthur J. de los Santos, Carlos Grollman, Arthur Zharkov, Dmitry O. Simmerling, Carlos |
author_facet | Li, Haoquan Endutkin, Anton V. Bergonzo, Christina Campbell, Arthur J. de los Santos, Carlos Grollman, Arthur Zharkov, Dmitry O. Simmerling, Carlos |
author_sort | Li, Haoquan |
collection | PubMed |
description | In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in the enzyme–DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for such mechanism is limited to a few systems. We report that discrimination between the oxidative DNA lesion, 8-oxoguanine (oxoG) and its normal counterpart, guanine, by the repair enzyme, formamidopyrimidine-DNA glycosylase (Fpg), likely involves multiple gates. Fpg uses an aromatic wedge to open the Watson–Crick base pair and everts the lesion into its active site. We used molecular dynamics simulations to explore the eversion free energy landscapes of oxoG and G by Fpg, focusing on structural and energetic details of oxoG recognition. The resulting energy profiles, supported by biochemical analysis of site-directed mutants disturbing the interactions along the proposed path, show that Fpg selectively facilitates eversion of oxoG by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation. Lesion recognition through multiple gating intermediates may be a common theme in DNA repair enzymes. |
format | Online Article Text |
id | pubmed-4737139 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-47371392016-02-03 A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase Li, Haoquan Endutkin, Anton V. Bergonzo, Christina Campbell, Arthur J. de los Santos, Carlos Grollman, Arthur Zharkov, Dmitry O. Simmerling, Carlos Nucleic Acids Res Genome Integrity, Repair and Replication In contrast to proteins recognizing small-molecule ligands, DNA-dependent enzymes cannot rely solely on interactions in the substrate-binding centre to achieve their exquisite specificity. It is widely believed that substrate recognition by such enzymes involves a series of conformational changes in the enzyme–DNA complex with sequential gates favoring cognate DNA and rejecting nonsubstrates. However, direct evidence for such mechanism is limited to a few systems. We report that discrimination between the oxidative DNA lesion, 8-oxoguanine (oxoG) and its normal counterpart, guanine, by the repair enzyme, formamidopyrimidine-DNA glycosylase (Fpg), likely involves multiple gates. Fpg uses an aromatic wedge to open the Watson–Crick base pair and everts the lesion into its active site. We used molecular dynamics simulations to explore the eversion free energy landscapes of oxoG and G by Fpg, focusing on structural and energetic details of oxoG recognition. The resulting energy profiles, supported by biochemical analysis of site-directed mutants disturbing the interactions along the proposed path, show that Fpg selectively facilitates eversion of oxoG by stabilizing several intermediate states, helping the rapidly sliding enzyme avoid full extrusion of every encountered base for interrogation. Lesion recognition through multiple gating intermediates may be a common theme in DNA repair enzymes. Oxford University Press 2016-01-29 2015-11-08 /pmc/articles/PMC4737139/ /pubmed/26553802 http://dx.doi.org/10.1093/nar/gkv1092 Text en © The Author(s) 2015. 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 | Genome Integrity, Repair and Replication Li, Haoquan Endutkin, Anton V. Bergonzo, Christina Campbell, Arthur J. de los Santos, Carlos Grollman, Arthur Zharkov, Dmitry O. Simmerling, Carlos A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase |
title | A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase |
title_full | A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase |
title_fullStr | A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase |
title_full_unstemmed | A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase |
title_short | A dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–DNA glycosylase |
title_sort | dynamic checkpoint in oxidative lesion discrimination by formamidopyrimidine–dna glycosylase |
topic | Genome Integrity, Repair and Replication |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4737139/ https://www.ncbi.nlm.nih.gov/pubmed/26553802 http://dx.doi.org/10.1093/nar/gkv1092 |
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