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Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69

DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases....

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Autores principales: Park, Jongseo, Youn, Hyung-Seop, An, Jun Yop, Lee, Youngjin, Eom, Soo Hyun, Wang, Jimin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8639217/
https://www.ncbi.nlm.nih.gov/pubmed/34869578
http://dx.doi.org/10.3389/fmolb.2021.704813
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author Park, Jongseo
Youn, Hyung-Seop
An, Jun Yop
Lee, Youngjin
Eom, Soo Hyun
Wang, Jimin
author_facet Park, Jongseo
Youn, Hyung-Seop
An, Jun Yop
Lee, Youngjin
Eom, Soo Hyun
Wang, Jimin
author_sort Park, Jongseo
collection PubMed
description DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed.
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spelling pubmed-86392172021-12-03 Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69 Park, Jongseo Youn, Hyung-Seop An, Jun Yop Lee, Youngjin Eom, Soo Hyun Wang, Jimin Front Mol Biosci Molecular Biosciences DNA polymerase plays a critical role in passing the genetic information of any living organism to its offspring. DNA polymerase from enterobacteria phage RB69 (RB69pol) has both polymerization and exonuclease activities and has been extensively studied as a model system for B-family DNA polymerases. Many binary and ternary complex structures of RB69pol are known, and they all contain a single polymerase-primer/template (P/T) DNA complex. Here, we report a crystal structure of the exonuclease-deficient RB69pol with the P/T duplex in a dimeric form at a resolution of 2.2 Å. The structure includes one new closed ternary complex with a single divalent metal ion bound and one new open binary complex in the pre-insertion state with a vacant dNTP-binding pocket. These complexes suggest that initial binding of the correct dNTP in the open state is much weaker than expected and that initial binding of the second divalent metal ion in the closed state is also much weaker than measured. Additional conformational changes are required to convert these complexes to high-affinity states. Thus, the measured affinities for the correct incoming dNTP and divalent metal ions are average values from many conformationally distinctive states. Our structure provides new insights into the order of the complex assembly involving two divalent metal ions. The biological relevance of specific interactions observed between one RB69pol and the P/T duplex bound to the second RB69pol observed within this dimeric complex is discussed. Frontiers Media S.A. 2021-11-18 /pmc/articles/PMC8639217/ /pubmed/34869578 http://dx.doi.org/10.3389/fmolb.2021.704813 Text en Copyright © 2021 Park, Youn, An, Lee, Eom and Wang. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Park, Jongseo
Youn, Hyung-Seop
An, Jun Yop
Lee, Youngjin
Eom, Soo Hyun
Wang, Jimin
Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
title Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
title_full Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
title_fullStr Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
title_full_unstemmed Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
title_short Structure of New Binary and Ternary DNA Polymerase Complexes From Bacteriophage RB69
title_sort structure of new binary and ternary dna polymerase complexes from bacteriophage rb69
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8639217/
https://www.ncbi.nlm.nih.gov/pubmed/34869578
http://dx.doi.org/10.3389/fmolb.2021.704813
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