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Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling

Abstract

In bacteria, the initiation of replication is controlled by DnaA, a member of the ATPases associated with various cellular activities (AAA+) protein superfamily. ATP binding allows DnaA to transition from a monomeric state into a large oligomeric complex that remodels replication origins, triggers duplex melting and facilitates replisome assembly. The crystal structure of AMP-PCP–bound DnaA reveals a right-handed superhelix defined by specific protein-ATP interactions. The observed quaternary structure of DnaA, along with topology footprint assays, indicates that a right-handed DNA wrap is formed around the initiation nucleoprotein complex. This model clarifies how DnaA engages and unwinds bacterial origins and suggests that additional, regulatory AAA+ proteins engage DnaA at filament ends. Eukaryotic and archaeal initiators also have the structural elements that promote open-helix formation, indicating that a spiral, open-ring AAA+ assembly forms the core element of initiators in all domains of life.

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Figure 1: Structure of ATP-DnaA.
Figure 2: Organization of AAA+ modules in the helical filament.
Figure 3: A functional, closed nucleotide-interaction pocket in ATP-DnaA.
Figure 4: The initiator helical insert drives filament formation.
Figure 5: Conformational changes induced by ATP binding.
Figure 6: The DnaA filament in the context of the nucleoprotein complex.
Figure 7: Hda has a conserved box VII motif that is essential for regulation of DnaA.

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Acknowledgements

We thank J. Holton and J. Tanamachi for support at Advanced Light Source beamline 8.3.1 and A. Schoeffler for purifying Topo IB. N. Cozzarelli, M. Botchan, J. Kuriyan, J. Keck, J. Stray and members of the Berger laboratory provided helpful comments and suggestions. This work was supported by the G. Harold and Leila Y. Mathers Charitable Foundation and the US National Institutes of Health (GM071747).

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Correspondence to James M Berger.

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Supplementary information

Supplementary Fig. 1

Representative electron density. (PDF 725 kb)

Supplementary Fig. 2

Aquifex aeolicus origin organization. (PDF 77 kb)

Supplementary Fig. 3

Surface characteristics of the ATP-DnaA filament. (PDF 404 kb)

Supplementary Video 1

Filament structure. (MOV 11654 kb)

Supplementary Video 2

Animation of ADP-to-ATP transition. (MOV 18017 kb)

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Erzberger, J., Mott, M. & Berger, J. Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling. Nat Struct Mol Biol 13, 676–683 (2006). https://doi.org/10.1038/nsmb1115

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