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The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer

Author

Listed:
  • Almutasem Saleh

    (Imperial College London)

  • Yasunori Noguchi

    (Imperial College London)

  • Ricardo Aramayo

    (Imperial College London)

  • Marina E. Ivanova

    (Imperial College London)

  • Kathryn M. Stevens

    (Imperial College London
    MRC London Institute of Medical Sciences (LMS))

  • Alex Montoya

    (Hammersmith Hospital Campus)

  • S. Sunidhi

    (InstaDeep Ltd, 5 Merchant Square)

  • Nicolas Lopez Carranza

    (InstaDeep Ltd, 5 Merchant Square)

  • Marcin J. Skwark

    (InstaDeep Ltd, 5 Merchant Square)

  • Christian Speck

    (Imperial College London
    MRC London Institute of Medical Sciences (LMS))

Abstract

The controlled assembly of replication forks is critical for genome stability. The Dbf4-dependent Cdc7 kinase (DDK) initiates replisome assembly by phosphorylating the MCM2-7 replicative helicase at the N-terminal tails of Mcm2, Mcm4 and Mcm6. At present, it remains poorly understood how DDK docks onto the helicase and how the kinase targets distal Mcm subunits for phosphorylation. Using cryo-electron microscopy and biochemical analysis we discovered that an interaction between the HBRCT domain of Dbf4 with Mcm2 serves as an anchoring point, which supports binding of DDK across the MCM2-7 double-hexamer interface and phosphorylation of Mcm4 on the opposite hexamer. Moreover, a rotation of DDK along its anchoring point allows phosphorylation of Mcm2 and Mcm6. In summary, our work provides fundamental insights into DDK structure, control and selective activation of the MCM2-7 helicase during DNA replication. Importantly, these insights can be exploited for development of novel DDK inhibitors.

Suggested Citation

  • Almutasem Saleh & Yasunori Noguchi & Ricardo Aramayo & Marina E. Ivanova & Kathryn M. Stevens & Alex Montoya & S. Sunidhi & Nicolas Lopez Carranza & Marcin J. Skwark & Christian Speck, 2022. "The structural basis of Cdc7-Dbf4 kinase dependent targeting and phosphorylation of the MCM2-7 double hexamer," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
  • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-30576-1
    DOI: 10.1038/s41467-022-30576-1
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    1. Sidhartha Chaudhury & Monica Berrondo & Brian D Weitzner & Pravin Muthu & Hannah Bergman & Jeffrey J Gray, 2011. "Benchmarking and Analysis of Protein Docking Performance in Rosetta v3.2," PLOS ONE, Public Library of Science, vol. 6(8), pages 1-13, August.
    2. Max E. Douglas & Ferdos Abid Ali & Alessandro Costa & John F. X. Diffley, 2018. "The mechanism of eukaryotic CMG helicase activation," Nature, Nature, vol. 555(7695), pages 265-268, March.
    3. Yi-Jun Sheu & Bruce Stillman, 2010. "The Dbf4–Cdc7 kinase promotes S phase by alleviating an inhibitory activity in Mcm4," Nature, Nature, vol. 463(7277), pages 113-117, January.
    4. Zuanning Yuan & Roxana Georgescu & Lin Bai & Dan Zhang & Huilin Li & Michael E. O’Donnell, 2020. "DNA unwinding mechanism of a eukaryotic replicative CMG helicase," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    5. Mary E. Dickinson & Ann M. Flenniken & Xiao Ji & Lydia Teboul & Michael D. Wong & Jacqueline K. White & Terrence F. Meehan & Wolfgang J. Weninger & Henrik Westerberg & Hibret Adissu & Candice N. Baker, 2016. "High-throughput discovery of novel developmental phenotypes," Nature, Nature, vol. 537(7621), pages 508-514, September.
    6. Ferdos Abid Ali & Max E. Douglas & Julia Locke & Valerie E. Pye & Andrea Nans & John F. X. Diffley & Alessandro Costa, 2017. "Cryo-EM structure of a licensed DNA replication origin," Nature Communications, Nature, vol. 8(1), pages 1-10, December.
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    1. Zhichun Xu & Jianrong Feng & Daqi Yu & Yunjing Huo & Xiaohui Ma & Wai Hei Lam & Zheng Liu & Xiang David Li & Toyotaka Ishibashi & Shangyu Dang & Yuanliang Zhai, 2023. "Synergism between CMG helicase and leading strand DNA polymerase at replication fork," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    2. Matthew Day & Bilal Tetik & Milena Parlak & Yasser Almeida-Hernández & Markus Räschle & Farnusch Kaschani & Heike Siegert & Anika Marko & Elsa Sanchez-Garcia & Markus Kaiser & Isabel A. Barker & Laure, 2024. "TopBP1 utilises a bipartite GINS binding mode to support genome replication," Nature Communications, Nature, vol. 15(1), pages 1-20, December.

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