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Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity

[Image: see text] DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase κ (Polκ), a member of the Y family of lesion bypass polymerases, is specialized to...

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Autores principales: Lior-Hoffmann, Lee, Ding, Shuang, Geacintov, Nicholas E., Zhang, Yingkai, Broyde, Suse
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Chemical Society 2014
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159208/
https://www.ncbi.nlm.nih.gov/pubmed/25148552
http://dx.doi.org/10.1021/bi5007964
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author Lior-Hoffmann, Lee
Ding, Shuang
Geacintov, Nicholas E.
Zhang, Yingkai
Broyde, Suse
author_facet Lior-Hoffmann, Lee
Ding, Shuang
Geacintov, Nicholas E.
Zhang, Yingkai
Broyde, Suse
author_sort Lior-Hoffmann, Lee
collection PubMed
description [Image: see text] DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase κ (Polκ), a member of the Y family of lesion bypass polymerases, is specialized to bypass bulky DNA minor groove lesions in a predominantly error-free manner, by housing them in its unique gap. We have investigated the role of the unique Polκ gap and N-clasp structural features in the fidelity of minor groove lesion processing with extensive molecular modeling and molecular dynamics simulations to pinpoint their functioning in lesion bypass. Here we consider the N(2)-dG covalent adduct derived from the carcinogenic aromatic amine, 2-acetylaminofluorene (dG-N(2)-AAF), that is produced via the combustion of kerosene and diesel fuel. Our simulations reveal how the spacious gap directionally accommodates the lesion aromatic ring system as it transits through the stages of incorporation of the predominant correct partner dCTP opposite the damaged guanine, with preservation of local active site organization for nucleotidyl transfer. Furthermore, flexibility in Polκ’s N-clasp facilitates the significant misincorporation of dTTP opposite dG-N(2)-AAF via wobble pairing. Notably, we show that N-clasp flexibility depends on lesion topology, being markedly reduced in the case of the benzo[a]pyrene-derived major adduct to N(2)-dG, whose bypass by Polκ is nearly error-free. Thus, our studies reveal how Polκ’s unique structural and dynamic properties can regulate its bypass fidelity of polycyclic aromatic lesions and how the fidelity is impacted by lesion structures.
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spelling pubmed-41592082015-08-19 Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity Lior-Hoffmann, Lee Ding, Shuang Geacintov, Nicholas E. Zhang, Yingkai Broyde, Suse Biochemistry [Image: see text] DNA lesion bypass polymerases process different lesions with varying fidelities, but the structural, dynamic, and mechanistic origins of this phenomenon remain poorly understood. Human DNA polymerase κ (Polκ), a member of the Y family of lesion bypass polymerases, is specialized to bypass bulky DNA minor groove lesions in a predominantly error-free manner, by housing them in its unique gap. We have investigated the role of the unique Polκ gap and N-clasp structural features in the fidelity of minor groove lesion processing with extensive molecular modeling and molecular dynamics simulations to pinpoint their functioning in lesion bypass. Here we consider the N(2)-dG covalent adduct derived from the carcinogenic aromatic amine, 2-acetylaminofluorene (dG-N(2)-AAF), that is produced via the combustion of kerosene and diesel fuel. Our simulations reveal how the spacious gap directionally accommodates the lesion aromatic ring system as it transits through the stages of incorporation of the predominant correct partner dCTP opposite the damaged guanine, with preservation of local active site organization for nucleotidyl transfer. Furthermore, flexibility in Polκ’s N-clasp facilitates the significant misincorporation of dTTP opposite dG-N(2)-AAF via wobble pairing. Notably, we show that N-clasp flexibility depends on lesion topology, being markedly reduced in the case of the benzo[a]pyrene-derived major adduct to N(2)-dG, whose bypass by Polκ is nearly error-free. Thus, our studies reveal how Polκ’s unique structural and dynamic properties can regulate its bypass fidelity of polycyclic aromatic lesions and how the fidelity is impacted by lesion structures. American Chemical Society 2014-08-19 2014-09-09 /pmc/articles/PMC4159208/ /pubmed/25148552 http://dx.doi.org/10.1021/bi5007964 Text en Copyright © 2014 American Chemical Society Terms of Use (http://pubs.acs.org/page/policy/authorchoice_termsofuse.html)
spellingShingle Lior-Hoffmann, Lee
Ding, Shuang
Geacintov, Nicholas E.
Zhang, Yingkai
Broyde, Suse
Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity
title Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity
title_full Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity
title_fullStr Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity
title_full_unstemmed Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity
title_short Structural and Dynamic Characterization of Polymerase κ’s Minor Groove Lesion Processing Reveals How Adduct Topology Impacts Fidelity
title_sort structural and dynamic characterization of polymerase κ’s minor groove lesion processing reveals how adduct topology impacts fidelity
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159208/
https://www.ncbi.nlm.nih.gov/pubmed/25148552
http://dx.doi.org/10.1021/bi5007964
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