A cohesin acetylation complex that recognises nicked DNA

Eukaryotic DNA replication products are held together by cohesin to enable their faithful inheritance during cell division. The establishment of stable sister chromatid cohesion requires replication-coupled acetylation of two conserved lysines on the cohesin Smc3 ATPase head. Here, we use AlphaFold 3 to predict the existence of a budding yeast cohesin acetylation complex, consisting of the replication protein PCNA, the cohesin subunit Pds5 and the Eco1 acetyltransferase. The predicted complex specifically contacts nicked DNA, a replication fork determinant that controls acetylation. Furthermore, cohesin engagement results in predicted conformational adaptations that bring acetyl-CoA in striking distance of the Smc3 target lysine. We perform biochemical and genetic experiments that confirm anticipated features of this reaction trajectory. Related cohesin acetylation complexes are predicted to form in other eukaryotes, including humans. Our study combines AI-assisted structure predictions and wet-bench experimentation to reveal the likely mechanism of replication-coupled cohesin acetylation during sister chromatid cohesion establishment.