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Structural analysis of a eukaryotic sliding DNA clamp–clamp loader complex

Abstract

Sliding clamps are ring-shaped proteins that encircle DNA and confer high processivity on DNA polymerases. Here we report the crystal structure of the five-protein clamp loader complex (replication factor-C, RFC) of the yeast Saccharomyces cerevisiae, bound to the sliding clamp (proliferating cell nuclear antigen, PCNA). Tight interfacial coordination of the ATP analogue ATP-γS by RFC results in a spiral arrangement of the ATPase domains of the clamp loader above the PCNA ring. Placement of a model for primed DNA within the central hole of PCNA reveals a striking correspondence between the RFC spiral and the grooves of the DNA double helix. This model, in which the clamp loader complex locks onto primed DNA in a screw-cap-like arrangement, provides a simple explanation for the process by which the engagement of primer–template junctions by the RFC:PCNA complex results in ATP hydrolysis and release of the sliding clamp on DNA.

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Figure 1: Overview of the RFC:PCNA complex.
Figure 2: The AAA + domains of the RFC assembly form a right-handed spiral.
Figure 3: Nucleotide is tightly bound between proximal and distal faces of the RFC-A and RFC-B AAA + modules.
Figure 4: A model for primed DNA interacting with the RFC:PCNA complex.
Figure 5: Conserved residues in domain I of clamp loader subunits at the proposed DNA-interacting surface.
Figure 6: Inactive and active clamp loader complexes.

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Acknowledgements

We thank J. Berger, E. Goedken, M. Hingorani, D. Jeruzalmi, A. Johnson, S. Kazmirski, I. Nodelman, M. Podobnik, N. Yao and M. Young for scientific discussions, S. Chung and J. Finkelstein for technical assistance, K. Morikawa for sharing data prior to publication, L. Leighton for help with figure preparation, D. King for mass spectroscopy analysis, and members of the Kuriyan laboratory for support and helpful discussions. We appreciate the assistance of C. Ralston, G. McDermott and the scientific staff of the Advanced Light Source (LBNL, Berkeley) in data collection. This work was supported by grants from the National Institutes of Health (J.K. and M.O.D.) and a Ruth L. Kirschstein National Research Service Award through the National Institute of General Medical Sciences (G.D.B.).

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Supplementary information

Supplementary Figure 1

Removal of the RFC “arginine finger” residues severely compromises the RFC ATPase. (JPG 18 kb)

Supplementary Figure 2

Experimental MAD-phased electron density maps surrounding bound nucleotides reveal the triphosphate character for RFC-A, B, C and D. (JPG 70 kb)

Supplementary Figure 3

The A:B interface of the RFC complex is more closely packed than those of NSF and HslU. (JPG 77 kb)

Supplementary Figure Legends (DOC 20 kb)

Supplementary Table (DOC 26 kb)

Supplementary Methods (DOC 23 kb)

Supplementary References

References for supplementary methods and figures. (DOC 20 kb)

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Bowman, G., O'Donnell, M. & Kuriyan, J. Structural analysis of a eukaryotic sliding DNA clamp–clamp loader complex. Nature 429, 724–730 (2004). https://doi.org/10.1038/nature02585

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