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    dNTP-dependent conformational transitions in the fingers subdomain of klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state

    Rothwell, P.J. and Allen, W.J. and Sisamakis, E. and Kalinin, S. and Felekyan, S. and Widengren, J. and Waksman, Gabriel and Seidel, C.A.M. (2013) dNTP-dependent conformational transitions in the fingers subdomain of klentaq1 DNA polymerase: insights into the role of the "nucleotide-binding" state. Journal of Biological Chemistry 288 (19), pp. 13575-13591. ISSN 0021-9258.

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    Background: Conformational selection plays a key role in the polymerase cycle. Results: Klentaq1 exists in conformational equilibrium between three states (open, closed, and “nucleotide-binding”) whose level of occupancy is determined by the bound substrate. Conclusion: The “nucleotide-binding” state plays a pivotal role in the reaction pathway. Significance: Direct evidence is provided for the role of a conformationally distinct “nucleotide-binding” state during dNTP incorporation. DNA polymerases are responsible for the accurate replication of DNA. Kinetic, single-molecule, and x-ray studies show that multiple conformational states are important for DNA polymerase fidelity. Using high precision FRET measurements, we show that Klentaq1 (the Klenow fragment of Thermus aquaticus DNA polymerase 1) is in equilibrium between three structurally distinct states. In the absence of nucleotide, the enzyme is mostly open, whereas in the presence of DNA and a correctly base-pairing dNTP, it re-equilibrates to a closed state. In the presence of a dNTP alone, with DNA and an incorrect dNTP, or in elevated MgCl2 concentrations, an intermediate state termed the "nucleotide-binding" state predominates. Photon distribution and hidden Markov modeling revealed fast dynamic and slow conformational processes occurring between all three states in a complex energy landscape suggesting a mechanism in which dNTP delivery is mediated by the nucleotide-binding state. After nucleotide binding, correct dNTPs are transported to the closed state, whereas incorrect dNTPs are delivered to the open state.


    Item Type: Article
    Keyword(s) / Subject(s): conformational selection, DNA enzymes, DNA polymerase, enzyme kinetics, fluorescence resonance energy transfer (FRET), single molecule biophysics
    School: Birkbeck Faculties and Schools > Faculty of Science > School of Natural Sciences
    Research Centres and Institutes: Structural Molecular Biology, Institute of (ISMB)
    Depositing User: Sarah Hall
    Date Deposited: 20 Jan 2014 13:59
    Last Modified: 02 Aug 2023 17:09


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