6QH1

The structure of Schizosaccharomyces pombe PCNA in complex with an Spd1 derived peptide

Summary for 6QH1

• Entry DOI: 10.2210/pdb6qh1/pdb
• Descriptor: Proliferating cell nuclear antigen, S-phase delaying protein 1 (2 entities in total)
• Functional Keywords: dna repair, dna replication, cell cycle regulation, pcna-spd1 complex, dna binding protein
• Biological source: Schizosaccharomyces pombe (Fission yeast); More
• Total number of polymer chains: 4
• Total formula weight: 88040.65

Authors

Kragelund, B.B.,Nielsen, O.,Olsen, J.G.,Kassem, N.,Prestel, A. (deposition date: 2019-01-14, release date: 2020-02-05, Last modification date: 2025-01-15)

Primary citation

Olsen, J.G.,Prestel, A.,Kassem, N.,Broendum, S.S.,Shamim, H.M.,Simonsen, S.,Grysbaek, M.,Mortensen, J.,Rytkjaer, L.L.,Haxholm, G.W.,Marabini, R.,Holmberg, C.,Carr, A.M.,Crehuet, R.,Nielsen, O.,Kragelund, B.B.
Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs.
Nucleic Acids Res., 52:2030-2044, 2024

PubMed Abstract: DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.

PubMed: 38261971
DOI: 10.1093/nar/gkae011

Experimental method

X-RAY DIFFRACTION (2.9 Å)