Cargando…

MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1

Apurinic/apyrimidinic endonuclease 1 (APE1), a central enzyme in the base excision repair pathway, cleaves damaged DNA in Mg(2+) dependent reaction. Despite characterization of nine X-ray crystallographic structures of human APE1, in some cases, bound to various metal ions and substrate/product, the...

Descripción completa

Detalles Bibliográficos
Autores principales: Oezguen, Numan, Mantha, Anil K, Izumi, Tadahide, Schein, Catherine H, Mitra, Sankar, Braun, Werner
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Biomedical Informatics 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218521/
https://www.ncbi.nlm.nih.gov/pubmed/22102776
_version_ 1782216697841713152
author Oezguen, Numan
Mantha, Anil K
Izumi, Tadahide
Schein, Catherine H
Mitra, Sankar
Braun, Werner
author_facet Oezguen, Numan
Mantha, Anil K
Izumi, Tadahide
Schein, Catherine H
Mitra, Sankar
Braun, Werner
author_sort Oezguen, Numan
collection PubMed
description Apurinic/apyrimidinic endonuclease 1 (APE1), a central enzyme in the base excision repair pathway, cleaves damaged DNA in Mg(2+) dependent reaction. Despite characterization of nine X-ray crystallographic structures of human APE1, in some cases, bound to various metal ions and substrate/product, the position of the metal ion and its stoichiometry for the cleavage reaction are still being debated. While a mutation of the active site E96Q was proposed to eliminate Mg(2+) binding at the “A” site, we show experimentally that this mutant still requires Mg(2+) at concentration similar to that for the wild type enzyme to cleave the AP site in DNA. Molecular dynamics simulations of the wild type APE1, E96Q and a double missense mutant E96Q + D210N indicate that Mg(2+) placed at the A-site destabilizes the bound AP site-containing DNA. In these simulations, the H-bond chain D238-H309-AP site oxygen is broken and the substrate DNA is shifted away from its crystal structure position (1DE9). In contrast, simulations with the Mg(2+) at site B or A+B sites leave the substrate DNA at the position shown in the crystal structure (1DE9). Taken together our MD simulations and biochemical analysis suggests that Mg(2+) binding at the B site is involved in the reaction mechanism associated with endonuclease function of APE1. ABBREVIATIONS: APE - AP-endonuclease, AP site - apurinic/apyrimidinic site, BER - base excision repair, Ref-1 - redox factor 1, hAPE1 - human APE1, WT - wild type, MD - molecular dynamics, THF - tetrahydrofuran.
format Online
Article
Text
id pubmed-3218521
institution National Center for Biotechnology Information
language English
publishDate 2011
publisher Biomedical Informatics
record_format MEDLINE/PubMed
spelling pubmed-32185212011-11-18 MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1 Oezguen, Numan Mantha, Anil K Izumi, Tadahide Schein, Catherine H Mitra, Sankar Braun, Werner Bioinformation Hypothesis Apurinic/apyrimidinic endonuclease 1 (APE1), a central enzyme in the base excision repair pathway, cleaves damaged DNA in Mg(2+) dependent reaction. Despite characterization of nine X-ray crystallographic structures of human APE1, in some cases, bound to various metal ions and substrate/product, the position of the metal ion and its stoichiometry for the cleavage reaction are still being debated. While a mutation of the active site E96Q was proposed to eliminate Mg(2+) binding at the “A” site, we show experimentally that this mutant still requires Mg(2+) at concentration similar to that for the wild type enzyme to cleave the AP site in DNA. Molecular dynamics simulations of the wild type APE1, E96Q and a double missense mutant E96Q + D210N indicate that Mg(2+) placed at the A-site destabilizes the bound AP site-containing DNA. In these simulations, the H-bond chain D238-H309-AP site oxygen is broken and the substrate DNA is shifted away from its crystal structure position (1DE9). In contrast, simulations with the Mg(2+) at site B or A+B sites leave the substrate DNA at the position shown in the crystal structure (1DE9). Taken together our MD simulations and biochemical analysis suggests that Mg(2+) binding at the B site is involved in the reaction mechanism associated with endonuclease function of APE1. ABBREVIATIONS: APE - AP-endonuclease, AP site - apurinic/apyrimidinic site, BER - base excision repair, Ref-1 - redox factor 1, hAPE1 - human APE1, WT - wild type, MD - molecular dynamics, THF - tetrahydrofuran. Biomedical Informatics 2011-10-14 /pmc/articles/PMC3218521/ /pubmed/22102776 Text en © 2011 Biomedical Informatics This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Hypothesis
Oezguen, Numan
Mantha, Anil K
Izumi, Tadahide
Schein, Catherine H
Mitra, Sankar
Braun, Werner
MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1
title MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1
title_full MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1
title_fullStr MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1
title_full_unstemmed MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1
title_short MD simulation and experimental evidence for Mg(2+) binding at the B site in human AP endonuclease 1
title_sort md simulation and experimental evidence for mg(2+) binding at the b site in human ap endonuclease 1
topic Hypothesis
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218521/
https://www.ncbi.nlm.nih.gov/pubmed/22102776
work_keys_str_mv AT oezguennuman mdsimulationandexperimentalevidenceformg2bindingatthebsiteinhumanapendonuclease1
AT manthaanilk mdsimulationandexperimentalevidenceformg2bindingatthebsiteinhumanapendonuclease1
AT izumitadahide mdsimulationandexperimentalevidenceformg2bindingatthebsiteinhumanapendonuclease1
AT scheincatherineh mdsimulationandexperimentalevidenceformg2bindingatthebsiteinhumanapendonuclease1
AT mitrasankar mdsimulationandexperimentalevidenceformg2bindingatthebsiteinhumanapendonuclease1
AT braunwerner mdsimulationandexperimentalevidenceformg2bindingatthebsiteinhumanapendonuclease1