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Mechanism of DNA translocation in a replicative hexameric helicase

Abstract

The E1 protein of papillomavirus is a hexameric ring helicase belonging to the AAA + family. The mechanism that couples the ATP cycle to DNA translocation has been unclear. Here we present the crystal structure of the E1 hexamer with single-stranded DNA discretely bound within the hexamer channel and nucleotides at the subunit interfaces. This structure demonstrates that only one strand of DNA passes through the hexamer channel and that the DNA-binding hairpins of each subunit form a spiral ‘staircase’ that sequentially tracks the oligonucleotide backbone. Consecutively grouped ATP, ADP and apo configurations correlate with the height of the hairpin, suggesting a straightforward DNA translocation mechanism. Each subunit sequentially progresses through ATP, ADP and apo states while the associated DNA-binding hairpin travels from the top staircase position to the bottom, escorting one nucleotide of single-stranded DNA through the channel. These events permute sequentially around the ring from one subunit to the next.

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Figure 1: Structure of the E1 hexameric helicase in complex with ssDNA and ADP.
Figure 2: DNA binding in the E1 hexameric helicase.
Figure 3: Intersubunit interactions and nucleotide binding.
Figure 4: Cartoon depiction of a coordinated escort mechanism for the E1 hexameric helicase.

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Acknowledgements

We thank H. Robinson (beamline X29) and A. Héroux (beamline X26C) for support with data collection at the National Synchrotron Light Source (NSLS) at Brookhaven National Laboratory. We also thank G. Hannon and A. Gann for critical reading of the manuscript, and B. Stillman, N. Tolia and members of the Joshua-Tor laboratory for discussions. The NSLS is supported by the US Department of Energy, Division of Materials Sciences and Division of Chemical Sciences. This work was supported by an NIH grant to L.J.

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Correspondence to Leemor Joshua-Tor.

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Coordinates and structure factors are deposited in the Protein Data Bank under accession code 2GXA. Reprints and permissions information is available at npg.nature.com/reprintsandpermissions. The authors declare no competing financial interests.

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Supplementary Notes

This file contains Supplementary Methods with 15 references, and Supplementary Figures S1–S7 and Supplementary Tables S1 and S2. (PDF 18051 kb)

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Enemark, E., Joshua-Tor, L. Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442, 270–275 (2006). https://doi.org/10.1038/nature04943

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