Crystal structure and mutational analysis of the Saccharomyces cerevisiae cell cycle regulatory protein Cks1: implications for domain swapping, anion binding and protein interactions

Abstract

Background: The Saccharomyces cerevisiae protein Cks1 (cyclin-dependent kinase subunit 1) is essential for cell-cycle progression. The biological function of Cks1 can be modulated by a switch between two distinct molecular assemblies: the single domain fold, which results from the closing of a β-hinge motif, and the intersubunit β-strand interchanged dimer, which arises from the opening of the β-hinge motif. The crystal structure of a cyclin-dependent kinase (Cdk) in complex with the human Cks homolog CksHs1 single-domain fold revealed the importance of conserved hydrophobic residues and charged residues within the β-hinge motif. Results: The 3.0 Å resolution Cks1 structure reveals the strict structural conservation of the Cks α/β-core fold and the β-hinge motif. The β hinge identified in the Cks1 structure includes a novel pivot and exposes a cluster of conserved tyrosine residues that are involved in Cdk binding but are sequestered in the β-interchanged Cks homolog suc1 dimer structure. This Cks1 structure confirms the conservation of the Cks anion-binding site, which interacts with sidechain residues from the C-terminal α helix of another subunit in the crystal. Conclusions: The Cks1 structure exemplifies the conservation of the β-interchanged dimer and the anion-binding site in evolutionarily distant yeast and human Cks homologs. Mutational analyses including in vivo rescue of CKS1 disruption support the dual functional roles of the β-hinge residue Glu94, which participates in Cdk binding, and of the anion-binding pocket that is located 22 Å away and on an opposite face to Glu94. The Cks1 structure suggests a biological role for the β-interchanged dimer and the anion-binding site in targeting Cdks to specific phosphoproteins during cell-cycle progression.