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Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase
Helicases are nucleic acid-unwinding enzymes involved in the maintenance of genome integrity. Helicases share several “helicase motifs” that are highly conserved amino acid sequences and are classified into six superfamilies (SFs). The helicase SFs are further grouped into two classes based on their...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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The Biophysical Society of Japan
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8967476/ https://www.ncbi.nlm.nih.gov/pubmed/35435650 http://dx.doi.org/10.2142/biophysico.bppb-v19.0006 |
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author | Yokota, Hiroaki |
author_facet | Yokota, Hiroaki |
author_sort | Yokota, Hiroaki |
collection | PubMed |
description | Helicases are nucleic acid-unwinding enzymes involved in the maintenance of genome integrity. Helicases share several “helicase motifs” that are highly conserved amino acid sequences and are classified into six superfamilies (SFs). The helicase SFs are further grouped into two classes based on their functional units. One class that includes SFs 3–6 functions as a hexamer that can form a ring around DNA. Another class that includes SFs 1 and 2 functions in a non-hexameric form. The high homology in the primary and tertiary structures among SF1 helicases suggests that SF1 helicases have a common underlying mechanism. However, two opposing models for the functional unit, monomer and dimer models, have been proposed to explain DNA unwinding by SF1 helicases. This paper briefly describes the classification of helicase SFs and discusses the structural homology and the two opposing non-hexameric helicase models of SF1 helicases by focusing on Escherichia coli SF1 helicase UvrD, which plays a significant role in both nucleotide-excision repair and methyl-directed mismatch repair. This paper reviews past and recent studies on UvrD, including the author's single-molecule direct visualization of wild-type UvrD and a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C), the latter of which was used in genetic and biochemical assays that supported the monomer model. The visualization revealed that multiple UvrDΔ40C molecules jointly unwind DNA, presumably in an oligomeric form, similar to wild-type UvrD. Therefore, single-molecule direct visualization of nucleic acid-binding proteins can provide quantitative and kinetic information to reveal their fundamental mechanisms. |
format | Online Article Text |
id | pubmed-8967476 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | The Biophysical Society of Japan |
record_format | MEDLINE/PubMed |
spelling | pubmed-89674762022-04-15 Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase Yokota, Hiroaki Biophys Physicobiol Review Article (Invited) Helicases are nucleic acid-unwinding enzymes involved in the maintenance of genome integrity. Helicases share several “helicase motifs” that are highly conserved amino acid sequences and are classified into six superfamilies (SFs). The helicase SFs are further grouped into two classes based on their functional units. One class that includes SFs 3–6 functions as a hexamer that can form a ring around DNA. Another class that includes SFs 1 and 2 functions in a non-hexameric form. The high homology in the primary and tertiary structures among SF1 helicases suggests that SF1 helicases have a common underlying mechanism. However, two opposing models for the functional unit, monomer and dimer models, have been proposed to explain DNA unwinding by SF1 helicases. This paper briefly describes the classification of helicase SFs and discusses the structural homology and the two opposing non-hexameric helicase models of SF1 helicases by focusing on Escherichia coli SF1 helicase UvrD, which plays a significant role in both nucleotide-excision repair and methyl-directed mismatch repair. This paper reviews past and recent studies on UvrD, including the author's single-molecule direct visualization of wild-type UvrD and a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C), the latter of which was used in genetic and biochemical assays that supported the monomer model. The visualization revealed that multiple UvrDΔ40C molecules jointly unwind DNA, presumably in an oligomeric form, similar to wild-type UvrD. Therefore, single-molecule direct visualization of nucleic acid-binding proteins can provide quantitative and kinetic information to reveal their fundamental mechanisms. The Biophysical Society of Japan 2022-03-10 /pmc/articles/PMC8967476/ /pubmed/35435650 http://dx.doi.org/10.2142/biophysico.bppb-v19.0006 Text en 2022 THE BIOPHYSICAL SOCIETY OF JAPAN https://creativecommons.org/licenses/by-nc-sa/4.0/This article is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit
https://creativecommons.org/licenses/by-nc-sa/4.0/. |
spellingShingle | Review Article (Invited) Yokota, Hiroaki Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase |
title | Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase |
title_full | Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase |
title_fullStr | Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase |
title_full_unstemmed | Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase |
title_short | Quantitative and kinetic single-molecule analysis of DNA unwinding by Escherichia coli UvrD helicase |
title_sort | quantitative and kinetic single-molecule analysis of dna unwinding by escherichia coli uvrd helicase |
topic | Review Article (Invited) |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8967476/ https://www.ncbi.nlm.nih.gov/pubmed/35435650 http://dx.doi.org/10.2142/biophysico.bppb-v19.0006 |
work_keys_str_mv | AT yokotahiroaki quantitativeandkineticsinglemoleculeanalysisofdnaunwindingbyescherichiacoliuvrdhelicase |