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A sensor complements the steric gate when DNA polymerase ϵ discriminates ribonucleotides
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
Department of Chemistry - BMC, Uppsala University, Box 576, Uppsala, Sweden; Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, Copenhagen, Denmark.
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
Umeå University, Faculty of Medicine, Department of Medical Biochemistry and Biophysics.
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2023 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 51, no 20, p. 11225-11238Article in journal (Refereed) Published
Abstract [en]

The cellular imbalance between high concentrations of ribonucleotides (NTPs) and low concentrations of deoxyribonucleotides (dNTPs), is challenging for DNA polymerases when building DNA from dNTPs. It is currently believed that DNA polymerases discriminate against NTPs through a steric gate model involving a clash between a tyrosine and the 2′-hydroxyl of the ribonucleotide in the polymerase active site in B-family DNA polymerases. With the help of crystal structures of a B-family polymerase with a UTP or CTP in the active site, molecular dynamics simulations, biochemical assays and yeast genetics, we have identified a mechanism by which the finger domain of the polymerase sense NTPs in the polymerase active site. In contrast to the previously proposed polar filter, our experiments suggest that the amino acid residue in the finger domain senses ribonucleotides by steric hindrance. Furthermore, our results demonstrate that the steric gate in the palm domain and the sensor in the finger domain are both important when discriminating NTPs. Structural comparisons reveal that the sensor residue is conserved among B-family polymerases and we hypothesize that a sensor in the finger domain should be considered in all types of DNA polymerases.

Place, publisher, year, edition, pages
Oxford University Press, 2023. Vol. 51, no 20, p. 11225-11238
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Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:umu:diva-218101DOI: 10.1093/nar/gkad817PubMedID: 37819038Scopus ID: 2-s2.0-85178042069OAI: oai:DiVA.org:umu-218101DiVA, id: diva2:1819818
Funder
Vinnova, 2018-04969Swedish Research Council Formas, 2019-02496Swedish Cancer Society, 2018-05973Swedish Research Council, 2018-07152Swedish Research Council, 2019-03499Swedish Research Council, 2021-01104Available from: 2023-12-15 Created: 2023-12-15 Last updated: 2024-07-02Bibliographically approved

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Parkash, VimalBylund, Göran O.Osterman, PiaJohansson, Erik

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